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1
Nagaki, Kiyotaka, Junqi Song, Robert M. Stupar, Alexander S. Parokonny, Qiaoping Yuan, Shu Ouyang, Jia Liu, et al. "Molecular and Cytological Analyses of Large Tracks of Centromeric DNA Reveal the Structure and Evolutionary Dynamics of Maize Centromeres." Genetics 163, no. 2 (February 1, 2003): 759–70. http://dx.doi.org/10.1093/genetics/163.2.759.
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Abstract We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of ∼200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that were expanded by retrotransposon invasions. Seven centromere-specific retrotransposons of maize (CRM) were found in BAC 16H10. The CRM elements inserted randomly into either CentC monomers or other retrotransposons. Sequence comparisons of the long terminal repeats (LTRs) of individual CRM elements indicated that these elements transposed within the last 1.22 million years. We observed that all of the previously reported centromere-specific retrotransposons in rice and barley, which belong to the same family as the CRM elements, also recently transposed with the oldest element having transposed ∼3.8 million years ago. Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family.
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Zhu, Hua, Minou Nowrousian, Doris Kupfer, Hildur V. Colot, Gloria Berrocal-Tito, Hongshing Lai, Deborah Bell-Pedersen, Bruce A. Roe, Jennifer J. Loros, and Jay C. Dunlap. "Analysis of Expressed Sequence Tags From Two Starvation, Time-of-Day-Specific Libraries of Neurospora crassa Reveals Novel Clock-Controlled Genes." Genetics 157, no. 3 (March 1, 2001): 1057–65. http://dx.doi.org/10.1093/genetics/157.3.1057.
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Abstract In an effort to determine genes that are expressed in mycelial cultures of Neurospora crassa over the course of the circadian day, we have sequenced 13,000 cDNA clones from two time-of-day-specific libraries (morning and evening library) generating ∼20,000 sequences. Contig analysis allowed the identification of 445 unique expressed sequence tags (ESTs) and 986 ESTs present in multiple cDNA clones. For ∼50% of the sequences (710 of 1431), significant matches to sequences in the National Center for Biotechnology Information database (of known or unknown function) were detected. About 50% of the ESTs (721 of 1431) showed no similarity to previously identified genes. We hybridized Northern blots with probes derived from 26 clones chosen from contigs identified by multiple cDNA clones and EST sequences. Using these sequences, the representation of genes among the morning and evening sequences, respectively, in most cases does not reflect their expression patterns over the course of the day. Nevertheless, we were able to identify four new clock-controlled genes. On the basis of these data we predict that a significant proportion of the expressed Neurospora genes may be regulated by the circadian clock. The mRNA levels of all four genes peak in the subjective morning as is the case with previously identified ccgs.
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Theis, James F., Chen Yang, Christopher B. Schaefer, and Carol S. Newlon. "DNA Sequence and Functional Analysis of Homologous ARS Elements of Saccharomyces cerevisiae and S. carlsbergensis." Genetics 152, no. 3 (July 1, 1999): 943–52. http://dx.doi.org/10.1093/genetics/152.3.943.
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Abstract ARS elements of Saccharomyces cerevisiae are the cis-acting sequences required for the initiation of chromosomal DNA replication. Comparisons of the DNA sequences of unrelated ARS elements from different regions of the genome have revealed no significant DNA sequence conservation. We have compared the sequences of seven pairs of homologous ARS elements from two Saccharomyces species, S. cerevisiae and S. carlsbergensis. In all but one case, the ARS308-ARS308carl pair, significant blocks of homology were detected. In the cases of ARS305, ARS307, and ARS309, previously identified functional elements were found to be conserved in their S. carlsbergensis homologs. Mutation of the conserved sequences in the S. carlsbergensis ARS elements revealed that the homologous sequences are required for function. These observations suggested that the sequences important for ARS function would be conserved in other ARS elements. Sequence comparisons aided in the identification of the essential matches to the ARS consensus sequence (ACS) of ARS304, ARS306, and ARS310carl, though not of ARS310.
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Torroni, Antonio, Kirsi Huoponen, Paolo Francalacci, Maurizio Petrozzi, Laura Morelli, Rosaria Scozzari, Domenica Obinu, Marja-Liisa Savontaus, and Douglas C. Wallace. "Classification of European mtDNAs From an Analysis of Three European Populations." Genetics 144, no. 4 (December 1, 1996): 1835–50. http://dx.doi.org/10.1093/genetics/144.4.1835.
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Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations
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Cheng, Ya-Ming, and Bor-Yaw Lin. "Molecular Organization of Large Fragments in the Maize B Chromosome: Indication of a Novel Repeat." Genetics 166, no. 4 (April 1, 2004): 1947–61. http://dx.doi.org/10.1093/genetics/166.4.1947.
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Abstract The supernumerary B chromosome has no apparent effects on plant growth, and its molecular makeup is difficult to unravel, due to its high homology to the normal complement, which prevents conventional cloning. This difficulty was overcome previously by microdissecting the B chromosome under the microscope to result in 19 B clones, one of which is B specific and highly repetitive, dispersing over one-third of the B long arm and most regions of the centromeric knob. To gain insights into the molecular structure of the B chromosome, this sequence was used to screen a genomic library constructed from W22 carrying 16 B’s. Five clones (>10 kb each) were isolated, and all were repetitive, showing homology with A chromosomes in Southern and FISH analyses. Two of them were further characterized and sequenced. Each is composed of several restriction fragments with variable degrees of repetitiveness. Some of these are B specific and others have variable degrees of homology with the A chromosomes. The order of each characteristic group is not contiguous; they intersperse within those of other groups. Sequence analysis reveals that their sequences (∼26 kb) have no homology with any published gene other than sequences of transposable elements (retrotransposons and MITEs) and the B as well as the A centromeres. We uncovered a 1.6-kb CL-repeat sequence, seven units of which were present in the two clones in defective forms. Those repeats mostly arrange in tandem array in the B chromosome. Moreover, we detected transposition of a retrotransposon and a MITE element involved in the genesis of these two sequences.
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Cumberledge, Susan, and John Carbon. "Mutational Analysis of Meiotic and Mitotic Centromere Function in Saccharomyces cerevisiae." Genetics 117, no. 2 (October 1, 1987): 203–12. http://dx.doi.org/10.1093/genetics/117.2.203.
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ABSTRACT A centromere (CEN) in Saccharomyces cerevisiae consists of approximately 150 bp of DNA and contains 3 conserved sequence elements: a high A + T region 78-86 bp in length (element II), flanked on the left by a conserved 8-bp element I sequence (PuTCACPuTG), and on the right by a conserved 25-bp element III sequence. We have carried out a structure-function analysis of the element I and II regions of CEN3 by constructing mutations in these sequences and subsequently determining their effect on mitotic and meiotic chromosome segregation. We have also examined the mitotic and meiotic segregation behavior of ARS plasmids containing the structurally altered CEN3 sequences. Replacing the periodic tracts of A residues within element II with random A + T sequences of equal length increases the frequency of mitotic chromosome nondisjunction only 4-fold; whereas, reducing the A + T content of element II while preserving the length results in a 40-fold increase in the frequence of chromosome nondisjunction. Structural alterations in the element II region that do not decrease the overall length have little effect on the meiotic segregation behavior of the altered chromosomes. Centromeres containing a deletion of element I or a portion of element II retain considerable mitotic activity, yet plasmids carrying these same mutations segregate randomly during meiosis I, indicating these sequences to be essential for maintaining attachment of the replicated sister chromatids during the first meiotic division. The presence of an intact element I sequence properly spaced from the element III region is absolutely essential for proper meiotic function of the centromere.
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Kletzin, Arnulf, Angelika Lieke, Tim Urich, Robert L. Charlebois, and Christoph W. Sensen. "Molecular Analysis of pDL10 from Acidianus ambivalens Reveals a Family of Related Plasmids from Extremely Thermophilic and Acidophilic Archaea." Genetics 152, no. 4 (August 1, 1999): 1307–14. http://dx.doi.org/10.1093/genetics/152.4.1307.
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Abstract The 7598-bp plasmid pDL10 from the extremely thermophilic, acidophilic, and chemolithoautotrophic Archaeon Acidianus ambivalens was sequenced. It contains 10 open reading frames (ORFs) organized in five putative operons. The deduced amino acid sequence of the largest ORF (909 aa) showed similarity to bacterial Rep proteins known from phages and plasmids with rolling-circle (RC) replication. From the comparison of the amino acid sequences, a novel family of RC Rep proteins was defined. The pDL10 Rep protein shared 45-80% identical residues with homologous protein genes encoded by the Sulfolobus islandicus plasmids pRN1 and pRN2. Two DNA regions capable of forming extended stem-loop structures were also conserved in the three plasmids (48-69% sequence identity). In addition, a putative plasmid regulatory protein gene (plrA) was found, which was conserved among the three plasmids and the conjugative Sulfolobus plasmid pNOB8. A homolog of this gene was also found in the chromosome of S. solfataricus. Single-stranded DNA of both pDL10 strands was detected with a mung bean nuclease protection assay using PCR detection of protected fragments, giving additional evidence for an RC mechanism of replication.
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Ashburner, M., S. Misra, J. Roote, S. E. Lewis, R. Blazej, T. Davis, C. Doyle, et al. "An Exploration of the Sequence of a 2.9-Mb Region of the Genome of Drosophila melanogaster: The Adh Region." Genetics 153, no. 1 (September 1, 1999): 179–219. http://dx.doi.org/10.1093/genetics/153.1.179.
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Abstract A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized “Adh region.” A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species.
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Allaby, Robin G., and Terence A. Brown. "Network Analysis Provides Insights Into Evolution of 5S rDNA Arrays in Triticum and Aegilops." Genetics 157, no. 3 (March 1, 2001): 1331–41. http://dx.doi.org/10.1093/genetics/157.3.1331.
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Abstract We have used network analysis to study gene sequences of the Triticum and Aegilops 5S rDNA arrays, as well as the spacers of the 5S-DNA-A1 and 5S-DNA-2 loci. Network analysis describes relationships between 5S rDNA sequences in a more realistic fashion than conventional tree building because it makes fewer assumptions about the direction of evolution, the extent of sexual isolation, and the pattern of ancestry and descent. The networks show that the 5S rDNA sequences of Triticum and Aegilops species are related in a reticulate manner around principal nodal sequences. The spacer networks have multiple principal nodes of considerable antiquity but the gene network has just one principal node, corresponding to the correct gene sequence. The networks enable orthologous groups of spacer sequences to be identified. When orthologs are compared it is seen that the patterns of intra- and interspecific diversity are similar for both genes and spacers. We propose that 5S rDNA arrays combine sequence conservation with a large store of mutant variations, the number of correct gene copies within an array being the result of neutral processes that act on gene and spacer regions together.
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Medhora, M., K. Maruyama, and D. L. Hartl. "Molecular and functional analysis of the mariner mutator element Mos1 in Drosophila." Genetics 128, no. 2 (June 1, 1991): 311–18. http://dx.doi.org/10.1093/genetics/128.2.311.
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Abstract The white-peach allele in Drosophila results from insertion of the transposable element mariner. The particular copy that is inserted in white-peach is an inactive copy referred to as the peach element. The peach element is excised at a high rate in the presence of active copies of mariner located elsewhere in the genome, and the excision of peach in somatic cells is recognized phenotypically by the occurrence of eye-color mosaicism in white-peach flies. Active mariner elements identified by their ability to induce high levels of white-peach mosaicism are denoted Mos (Mosaic) factors. We have sequenced and functionally analyzed the factor Mos1 originally identified in Drosophila mauritiana. The Mos1 element is 1286 base pairs in length, the same length as the peach element. It differs from the peach element in 11 nucleotide positions distributed throughout its length, including four amino acid replacements in the long open reading frame. Analysis of chimeric constructs between Mos1 and peach implies that functionally important differences occur in both the 5' and 3' halves of Mos1. A mariner element identical in sequence to Mos1 yields lower levels of mosaicism in transformants, implying that adjacent flanking sequences have important effects on Mos1 activity. Another mariner element, designated Ma351, isolated from a nonmosaic strain of D. mauritiana, differs from Mos1 in just three nucleotide positions. When introduced into the germline, Ma351 yields various levels of white-peach mosaicism depending on insertion site. These results imply that the activity of mariner elements is determined jointly by their own nucleotide sequences, by the effects of adjacent flanking sequences, and by longer-range position effects.
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Rina, M., and C. Savakis. "A cluster of vitellogenin genes in the Mediterranean fruit fly Ceratitis capitata: sequence and structural conservation in dipteran yolk proteins and their genes." Genetics 127, no. 4 (April 1, 1991): 769–80. http://dx.doi.org/10.1093/genetics/127.4.769.
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Abstract Four genes encoding the major egg yolk polypeptides of the Mediterranean fruit fly Ceratitis capitata, vitellogenins 1 and 2 (VG1 and VG2), were cloned, characterized and partially sequenced. The genes are located on the same region of chromosome 5 and are organized in pairs, each encoding the two polypeptides on opposite DNA strands. Restriction and nucleotide sequence analysis indicate that the gene pairs have arisen from an ancestral pair by a relatively recent duplication event. The transcribed part is very similar to that of the Drosophila melanogaster yolk protein genes Yp1, Yp2 and Yp3. The Vg1 genes have two introns at the same positions as those in D. melanogaster Yp3; the Vg2 genes have only one of the introns, as do D. melanogaster Yp1 and Yp2. Comparison of the five polypeptide sequences shows extensive homology, with 27% of the residues being invariable. The sequence similarity of the processed proteins extends in two regions separated by a nonconserved region of varying size. Secondary structure predictions suggest a highly conserved secondary structure pattern in the two regions, which probably correspond to structural and functional domains. The carboxy-end domain of the C. capitata proteins shows the same sequence similarities with triacyglycerol lipases that have been reported previously for the D. melanogaster yolk proteins. Analysis of codon usage shows significant differences between D. melanogaster and C. capitata vitellogenins with the latter exhibiting a less biased representation of synonymous codons.
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Ness, F., and M. Aigle. "RTM1: a member of a new family of telomeric repeated genes in yeast." Genetics 140, no. 3 (July 1, 1995): 945–56. http://dx.doi.org/10.1093/genetics/140.3.945.
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Abstract We have isolated a new yeast gene called RTM1 whose overexpression confers resistance to the toxicity of molasses. The RTM1 gene encodes a hydrophobic 34-kD protein that contains seven potential transmembrane-spanning segments. Analysis of a series of industrial strains shows that the sequence is present in multiple copies and in variable locations in the genome. RTM loci are always physically associated with SUC telomeric loci. The SUC-RTM sequences are located between X and Y' subtelomeric sequences at chromosome ends. Surprisingly RTM sequences are not detected in the laboratory strain X2180. The lack of this sequence is associated with the absence of any SUC telomeric gene previously described. This observation raises the question of the origin of this nonessential gene. The particular subtelomeric position might explain the SUC-RTM sequence amplification observed in the genome of yeasts used in industrial biomass or ethanol production with molasses as substrate. This SUC-RTM sequence dispersion seems to be a good example of genomic rearrangement playing a role in evolution and environmental adaptation in these industrial yeasts.
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Yang, Tae-Jin, Jung-Sun Kim, Ki-Byung Lim, Soo-Jin Kwon, Jin-A. Kim, Mina Jin, Jee Young Park, et al. "The KoreaBrassicaGenome Project: a Glimpse of theBrassicaGenome Based on Comparative Genome Analysis WithArabidopsis." Comparative and Functional Genomics 6, no. 3 (2005): 138–46. http://dx.doi.org/10.1002/cfg.465.
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A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is sequencing chromosome 1 (cytogenetically oriented chromosome #1) ofBrassica rapa. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones fromBrassicachromosome 1 revealed their homeologous partner regions on theArabidopsisgenome and a syntenic comparative map betweenBrassicachromosome 1 andArabidopsischromosomes.In silicochromosome walking and clone validation have been successfully applied to extending sequence contigs based on the comparative map and BAC end sequences. In addition, we have defined the (peri)centromeric heterochromatin blocks with centromeric tandem repeats, rDNA and centromeric retrotransposons. In-depth sequence analyses of five homeologous BAC clones and anArabidopsischromosomal region reveal overall co-linearity, with 82% sequence similarity. The data indicate that theBrassicagenome has undergone triplication and subsequent gene losses after the divergence ofArabidopsisandBrassica. Based on in-depth comparative genome analyses, we propose a comparative genomics approach for conquering theBrassicagenome. In 2005 we intend to construct an integrated physical map, including sequence information from 500 BAC clones and integration of fingerprinting data and end sequence data of more than 100 000 BAC clones. The sequences have been submitted to GenBank with accession numbers: 10 204 BAC ends of the KBrH library (CW978640–CW988843); KBrH138P04, AC155338; KBrH117N09, AC155337; KBrH097M21, AC155348; KBrH093K03, AC155347; KBrH081N08, AC155346; KBrH080L24, AC155345; KBrH077A05, AC155343; KBrH020D15, AC155340; KBrH015H17, AC155339; KBrH001H24, AC155335; KBrH080A08, AC155344; KBrH004D11, AC155341; KBrH117M18, AC146875; KBrH052O08, AC155342.
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Chang, Yueh-Long, Quanzhou Tao, Chantel Scheuring, Kejiao Ding, Khalid Meksem, and Hong-Bin Zhang. "An Integrated Map of Arabidopsis thaliana for Functional Analysis of Its Genome Sequence." Genetics 159, no. 3 (November 1, 2001): 1231–42. http://dx.doi.org/10.1093/genetics/159.3.1231.
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Abstract The genome of the model plant species Arabidopsis thaliana has recently been sequenced. To accelerate its current genome research, we developed a whole-genome, BAC/BIBAC-based, integrated physical, genetic, and sequence map of the A. thaliana ecotype Columbia. This new map was constructed from the clones of a new plant-transformation-competent BIBAC library and is integrated with the existing sequence map. The clones were restriction fingerprinted by DNA sequencing gel-based electrophoresis, assembled into contigs, and anchored to an existing genetic map. The map consists of 194 BAC/BIBAC contigs, spanning 126 Mb of the 130-Mb Arabidopsis genome. A total of 120 contigs, spanning 114 Mb, were anchored to the chromosomes of Arabidopsis. Accuracy of the integrated map was verified using the existing physical and sequence maps and numerous DNA markers. Integration of the new map with the sequence map has enabled gap closure of the sequence map and will facilitate functional analysis of the genome sequence. The method used here has been demonstrated to be sufficient for whole-genome physical mapping from large-insert random bacterial clones and thus is applicable to rapid development of whole-genome physical maps for other species.
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Cambareri, E. B., M. J. Singer, and E. U. Selker. "Recurrence of repeat-induced point mutation (RIP) in Neurospora crassa." Genetics 127, no. 4 (April 1, 1991): 699–710. http://dx.doi.org/10.1093/genetics/127.4.699.
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Abstract Duplicate DNA sequences in the genome of Neurospora crassa can be detected and mutated in the sexual phase of the life cycle by a process termed RIP (repeat-induced point mutation). RIP occurs in the haploid nuclei of fertilized, premeiotic cells before fusion of the parental nuclei. Both copies of duplications of gene-sized sequences are affected in the first generation at frequencies of approximately 50-100%. We investigated the extent to which sequences altered by RIP remain susceptible to this process in subsequent generations. Duplications continued to be sensitive to RIP, even after six generations. The fraction of progeny showing evidence of RIP decreased rapidly, however, apparently as a function of the extent of divergence of the duplicated sequences. Analysis of the stability of heteroduplexes of DNA altered by RIP and their native counterpart indicated that linked duplications diverged further than did unlinked duplications. DNA methylation, a common feature of sequences altered by RIP, did not seem to inhibit the process. A sequence that had become resistant to RIP was cloned and reintroduced into Neurospora in one or more copies to investigate the basis of the resistance. The altered sequence regained its methylation in vegetative cells, indicating that the methylation of sequences altered by RIP observed in vegetative cells is a consequence of the mutations. Duplication of the sequence restored its sensitivity to RIP suggesting that resistance to the process was due to loss of similarity between the duplicated sequences. Consistent with this, we found that the resistant sequence did not trigger RIP of the native homologous sequences of the host, even when no other partner was available. High frequency intrachromatid recombination, which is temporally associated with RIP, was more sensitive than RIP to alterations in the interacting sequences.
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Huang, Yi, Susanna K. P. Lau, Patrick C. Y. Woo, and Kwok-yung Yuen. "CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes." Nucleic Acids Research 36, Supplement_1 (October 2, 2007): D504—D511. http://dx.doi.org/10.1093/nar/gkm754.
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Abstract The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.
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Alfenito, M. R., and J. A. Birchler. "Molecular characterization of a maize B chromosome centric sequence." Genetics 135, no. 2 (October 1, 1993): 589–97. http://dx.doi.org/10.1093/genetics/135.2.589.
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Abstract Supernumerary chromosomes are widespread in the plant kingdom but little is known of their molecular nature or mechanism of origin. We report here the initial cloning of sequences from the maize B chromosome. Our analysis suggests that many sequences are highly repetitive and shared with the normal A chromosomes. However, all clones selected for B-specificity contain at least one copy of a particular repeat. Cytological mapping using B chromosome derivatives and in situ hybridization show that the B specific repeats are derived from the centric region of the chromosome. Sequence analysis of this repeat shows homology to motifs mapped to various plant and animal centromeres and to the maize neocentromere. A precise localization of these sequences among breakpoints within the B centromere and an homology to a facultative centromere, suggest a role for this sequence in centromere function.
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Arkhipova, I. R. "Promoter elements in Drosophila melanogaster revealed by sequence analysis." Genetics 139, no. 3 (March 1, 1995): 1359–69. http://dx.doi.org/10.1093/genetics/139.3.1359.
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Abstract A Drosophila Promoter Database containing 252 independent Drosophila melanogaster promoter entries has been compiled. The database and its subsets have been searched for overrepresented sequences. The analysis reveals that the proximal promoter region displays the most dramatic nucleotide sequence irregularities and exhibits a tripartite structure, consisting of TATA at -25/-30 bp, initiator (Inr) at +/- 5 bp and a novel class of downstream elements at +20/+30 bp from the RNA start site. These latter elements are also strand-specific. However, they differ from TATA and Inr in several aspects: (1) they are represented not by a single, but by multiple sequences, (2) they are shorter, (3) their position is less strictly fixed with respect to the RNA start site, (4) they emerge as a characteristic feature of Drosophila promoters and (5) some of them are strongly overrepresented in the TATA-less, but not TATA-containing, subset. About one-half of known Drosophila promoters can be classified as TATA-less. The overall sequence organization of the promoter region is characterized by an extended region with an increase in GC-content and a decrease in A, which contains a number of binding sites for Drosophila transcription factors.
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Wang, M. L., J. A. Mosjidis, J. B. Morris, R. E. Dean, T. M. Jenkins, and G. A. Pederson. "Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers." Genome 49, no. 6 (June 1, 2006): 707–15. http://dx.doi.org/10.1139/g06-027.
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The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.Key words: Crotalaria germplasm, EST-SSR, genetic diversity, phylogeny.
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Danilevskaya, O., A. Lofsky, E. V. Kurenova, and M. L. Pardue. "The Y chromosome of Drosophila melanogaster contains a distinctive subclass of Het-A-related repeats." Genetics 134, no. 2 (June 1, 1993): 531–43. http://dx.doi.org/10.1093/genetics/134.2.531.
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Abstract The HeT-A element is a transposable element with an apparent role in the structure of the telomeres of Drosophila melanogaster chromosomes. HeT-A transposition is the earliest event detected in healing of broken ends; HeT-A is also found on telomeres of unbroken chromosomes. Sequences with homology to HeT-A are never detected in euchromatic regions; however, clusters of HeT-A-related sequences occur in nontelomeric regions of the heterochromatic Y chromosome. Analysis of two of these Y-associated clusters shows them to be significantly different in structure from telomeric HeT-A elements, although the regions of shared sequence have > 80% sequence identity in all cases. Telomeric HeT-A elements occur in chains, with the elements in the same orientation but variably truncated at their external ends and irregularly interspersed with unrelated sequences. In contrast, the nontelomeric Y elements are regular tandem repeats of parts of the HeT-A sequence joined to unrelated sequences which are not the same in the two clusters studied. The sequence structures suggest that the nontelomeric clusters on the Y chromosome do not arise by the same transposition mechanism that forms the telomeric clusters; instead the clusters on the Y may arise by a mechanism that is used more generally in the evolution of Y chromosomes. Although the telomeric and nontelomeric clusters appear to be formed differently, both are enriched in parts of the HeT-A sequence which may be important in the structure of heterochromatin.
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Abel, K. J., and K. W. Gross. "Physical characterization of genetic rearrangements at the mouse renin loci." Genetics 124, no. 4 (April 1, 1990): 937–47. http://dx.doi.org/10.1093/genetics/124.4.937.
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Abstract Many inbred strains of mice have a single locus encoding renin, Ren-1, whereas other inbred strains have two tandemly linked loci, Ren-1 and Ren-2. Each of these renin genes in inbred mice exhibits a unique pattern of tissue-specific expression. As a prerequisite to understanding the structural basis for the expression differences, we have physically characterized the sequence organization of this chromosomal region in both types of strains. Pulsed field gel electrophoresis was initially used to compare the long-range structure of this region in C57BL/6 (Ren-1) and DBA/2 (Ren-1 + Ren-2) mice. The structure in both inbred strains is extremely similar, except for an additional 30 kb containing Ren-2 in DBA/2 mice. The boundaries of the extra 30-kb segment were sequenced and compared to homologous sequences flanking the Ren-1 alleles. This analysis identified the precise recombination site, and also the presence of a large insertion, between the renin loci in DBA/2. The renin gene duplication apparently resulted from recombination between sequences sharing little homology, suggesting that nonhomologous chromosomal breakage and rejoining may have been involved mechanistically in the event.
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Fletcher, L. D., J. M. McDowell, R. R. Tidwell, R. B. Meagher, and C. C. Dykstra. "Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii." Genetics 137, no. 3 (July 1, 1994): 743–50. http://dx.doi.org/10.1093/genetics/137.3.743.
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Abstract Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding gene were isolated and characterized from Pneumocystis carinii purified from immunosuppressed rat lungs. The nucleotide sequence encodes a protein of 376 amino acids. The predicted actin protein of P. carinii shares a high degree of conservation to other known actins. Only one major actin gene was found in P. carinii. The P. carinii actin sequence was compared with 30 other actin sequences. Gene phylogenies constructed using both neighbor-joining and protein parsimony methods places the P. carinii actin sequence closest to the majority of the fungi. Since the phylogenetic relationship of P. carinii to fungi and protists has been questioned, these data on the actin gene phylogeny support the grouping of P. carinii with the fungi.
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Veit, B., E. Vollbrecht, J. Mathern, and S. Hake. "A tandem duplication causes the Kn1-O allele of Knotted, a dominant morphological mutant of maize." Genetics 125, no. 3 (July 1, 1990): 623–31. http://dx.doi.org/10.1093/genetics/125.3.623.
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Abstract Molecular and genetic techniques are used to define Kn1-O, a mutation which interferes with the normal differentiation of vascular tissue in leaves. Sequences associated with a previously cloned allele, Kn1-2F11, were used as hybridization probes in a Southern analysis of Kn1-O. By this analysis, Kn1-O lacks the Ds2 transposable element that causes Kn1-2F11 but instead is associated with a sequence duplication. Sequence and restriction analysis of genomic clones show that the duplication consists of a tandem array of two 17-kb repeats. Analysis of Kn1-O derivatives indicates that the duplication itself conditions the mutant phenotype; a severely knotted line, Kn1-Ox, has gained a repeat unit to form a triplication, whereas normal derivatives have either lost a repeat unit or sustained insertions that disrupt the tandem duplication. These insertions map near the central junction of the tandem duplication, suggesting that the mutant phenotype results from the novel juxtaposition of sequences. We discuss models that relate the tandem duplication of sequences to altered gene expression.
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Taylor, Loverine P., and Virginia Walbot. "Isolation and Characterization of a 1.7-kb Transposable Element from a Mutator Line of Maize." Genetics 117, no. 2 (October 1, 1987): 297–307. http://dx.doi.org/10.1093/genetics/117.2.297.
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ABSTRACT We have cloned and sequenced a 1.7-kb Mu element from a Mutator line of maize and compared its structure to Mu1, a 1.4-kb element. With the exception of a 385-bp block of DNA present in the 1.7-kb element, these transposable elements are structurally similar, sharing terminally inverted and internal direct repeated sequences. Derivation of 1.4-kb elements from the 1.7-kb class via deletion of internal sequence is suggested by the finding that a portion of the extra DNA in Mu1.7 is part of a truncated direct repeat sequence in the 1.4-kb element. An abundant poly(A)+ RNA homologous to a portion of this extra DNA is present in several tissues of both Mutator and non-Mutator lines. Analysis of transcripts from an unstable mutant bronze1 (bz) allele containing a Mu1.7 element inserted in an exon of the gene detects three species of poly(A)+ RNA that hybridize to a Bz1 (Bronze) gene probe: the largest contains the entire Mu1.7 element in the Bz1 gene transcript; another appears to be a spliced, chimeric transcript; the smallest is normal size Bz1 mRNA. The latter is most likely encoded by the normal-size alleles detected by Southern analysis of tissue expressing purple pigment, suggesting that normal gene function is restored by excision of the Mu1.7 element.
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Kennedy, Patricia, and Michael W. Nachman. "Deleterious Mutations at the Mitochondrial ND3 Gene in South American Marsh Rats (Holochilus)." Genetics 150, no. 1 (September 1, 1998): 359–68. http://dx.doi.org/10.1093/genetics/150.1.359.
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Abstract Statistical analyses of DNA sequences have revealed patterns of nonneutral evolution in mitochondrial DNA of mice, humans, and Drosophila. Here we report patterns of mitochondrial sequence evolution in South American marsh rats (genus Holochilus). We sequenced the complete mitochondrial ND3 gene in 82 Holochilus brasiliensis and 21 H. vulpinus to test the neutral prediction that the ratio of nonsynonymous to synonymous nucleotide changes is the same within and between species. Within H. brasiliensis we observed a greater number of amino acid polymorphisms than expected based on interspecific comparisons. This contingency table analysis suggests that many amino acid polymorphisms are mildly deleterious. Several tests of the frequency distribution also revealed departures from a neutral, equilibrium model, and these departures were observed for both nonsynonymous and synonymous sites. In general, an excess of rare sites was observed, consistent with either a recent selective sweep or with populations not at mutation-drift equilibrium.
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Mismer, D., W. M. Michael, T. R. Laverty, and G. M. Rubin. "Analysis of the promoter of the Rh2 opsin gene in Drosophila melanogaster." Genetics 120, no. 1 (September 1, 1988): 173–80. http://dx.doi.org/10.1093/genetics/120.1.173.
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Abstract We have analyzed the cis-acting regulatory sequences of the Drosophila melanogaster Rh2 gene that encodes the protein component of a rhodopsin which is expressed in ocellar photoreceptor cells. DNA fragments containing the start point of transcription of the Rh2 gene were fused to either the Escherichia coli chloramphenicol acetyltransferase (CAT) or lacZ (beta-galactosidase) genes and introduced into the Drosophila germline by P-element-mediated transformation. Expression of the E. coli genes was then used to assay the ability of various sequences from the Rh2 gene to confer upon the indicator genes the Rh2 pattern of expression. Fragments containing between 4.3 kb and 183 bp upstream of the start of transcription plus the first 32 bp of the 5'-untranslated leader were found to result in nearly identical levels of head-specific CAT expression. Deletion of Rh2 sequences distal to position -112 bp resulted in loss of detectable CAT expression from these Rh2/CAT fusion constructs. We have, therefore, defined a region essential for head-specific expression of the Rh2 gene to a region extending from -183 to -112. We have determined the DNA sequence of the Rh2 promoter from -448 to +32 and have found an 11-bp sequence which is also present in the upstream flanking sequences of two other photoreceptor-specific genes (ninaE and ninaC). By histochemical staining of beta-galactosidase expressed under the control of the Rh2 promoter and by analyzing the effect of the ocelliless mutation on the expression of an Rh2/CAT fusion gene, we have been able to demonstrate that this promoter is active in ocelli.
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Kimura, Makoto, Takeshi Tokai, Gentaro Matsumoto, Makoto Fujimura, Hiroshi Hamamoto, Katsuyoshi Yoneyama, Takehiko Shibata, and Isamu Yamaguchi. "Trichothecene Nonproducer Gibberella Species Have Both Functional and Nonfunctional 3-O-Acetyltransferase Genes." Genetics 163, no. 2 (February 1, 2003): 677–84. http://dx.doi.org/10.1093/genetics/163.2.677.
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Abstract The trichothecene 3-O-acetyltransferase gene (FgTri101) required for trichothecene production by Fusarium graminearum is located between the phosphate permease gene (pho5) and the UTP-ammonia ligase gene (ura7). We have cloned and sequenced the pho5-to-ura7 regions from three trichothecene nonproducing Fusarium (i.e., F. oxysporum, F. moniliforme, and Fusarium species IFO 7772) that belong to the teleomorph genus Gibberella. BLASTX analysis of these sequences revealed portions of predicted polypeptides with high similarities to the TRI101 polypeptide. While FspTri101 (Fusarium species Tri101) coded for a functional 3-O-acetyltransferase, FoTri101 (F. oxysporum Tri101) and FmTri101 (F. moniliforme Tri101) were pseudogenes. Nevertheless, F. oxysporum and F. moniliforme were able to acetylate C-3 of trichothecenes, indicating that these nonproducers possess another as yet unidentified 3-O-acetyltransferase gene. By means of cDNA expression cloning using fission yeast, we isolated the responsible FoTri201 gene from F. oxysporum; on the basis of this sequence, FmTri201 has been cloned from F. moniliforme by PCR techniques. Both Tri201 showed only a limited level of nucleotide sequence similarity to FgTri101 and FspTri101. The existence of Tri101 in a trichothecene nonproducer suggests that this gene existed in the fungal genome before the divergence of producers from nonproducers in the evolution of Fusarium species.
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Drijver, Evert, Joep Stohr, Jaco Verweij, Carlo Verhulst, Francisca Velkers, Arjan Stegeman, Marjolein Bergh, Jan Kluytmans, and i.-Health Group. "Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands." Microorganisms 8, no. 11 (November 8, 2020): 1755. http://dx.doi.org/10.3390/microorganisms8111755.
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Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1–pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1–pST12 plasmids revealed a low number of SNP differences (range of 0–9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1–pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.
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Begum, RA, MT Alam, H. Jahan, and MS Alam. "Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh." Journal of Biodiversity Conservation and Bioresource Management 5, no. 1 (July 13, 2019): 25–30. http://dx.doi.org/10.3329/jbcbm.v5i1.42182.
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Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular.
J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30
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Mismer, Drzislav, and Gerald M. Rubin. "Analysis of the Promoter of the ninaE Opsin Gene in Drosophila melanogaster." Genetics 116, no. 4 (August 1, 1987): 565–78. http://dx.doi.org/10.1093/genetics/116.4.565.
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ABSTRACT We have analyzed the cis-acting regulatory sequences of the ninaE gene. This gene encodes the major Drosophila melanogasteropsin, the protein component of the primary chromophore of photoreceptor cells R1-R6 of the adult eye. DNA fragments containing the start point of transcription of the ninaE gene were fused to either the Escherichia coli chloramphenicol acetyltransferase or lacZ (β-galactosidase) gene and introduced into the Drosophila germline by P-element-mediated transformation. Expression of the E. coli genes was then used to assay the ability of various sequences from the ninaE gene to confer the ninaE pattern of expression. Fragments containing between 2.8 kb and 215 bp of the sequences upstream of the start of transcription plus the first 67 bp of the untranslated leader were able to direct nearly wild-type expression. We have identified three separable control regions in the ninaE promoter. The first, which has the properties of an enhancer element, is located between nucleotides -501 and -219. The removal of this sequence had little effect on promoter function; this sequence appears to be redundant. However, it appears to be able to substitute for the second control region which is located between nucleotides -215 and -162, and which also affects the level of output from this promoter. Removal of these two control regions resulted in a 30-fold decrease in expression; however tissue specificity was not affected. The third control region, located downstream from nucleotide -120, appears to be absolutely necessary for promoter function in the absence of the first two regulatory sequences. Examination of larvae containing fusion genes expressing β-galactosidase suggests that the ninaE gene is also expressed in a subset of cells in the larval photoreceptor organ.
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Durie, Brian GM, Julia Beck, Sundar Jagannath, Howard B. Urnovitz, and Ekkehard Schutz. "Personalized Genetic Monitoring of myeloma using analytic multivariate analysis of total Fully-Sequenced Circulating DNA." Blood 112, no. 11 (November 16, 2008): 5120. http://dx.doi.org/10.1182/blood.v112.11.5120.5120.
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Abstract There is no single sequence or breakpoint region linked to all patients with myeloma. It was thus elected to extract, amplify and fully sequence all (total) DNA present in circulating blood (CNA) using pyrosequencing with the Roche/454 sequencer (GSFLX). The origin of circulating DNA was investigated by local alignment analyses using BLAST and compared with the circulating DNA of 47 healthy individuals, aged 18 to 64 years. Thirty-one samples were subjected to total CNA sequencing during the course of the disease for a patient with lambda Bence Jones myeloma sequentially monitored from relapse, through complete response for 38 months and then with development of subsequent relapse. Conventional monitoring included both serum free light chain analyses and whole body CT-PET imaging. For comparative purposes the CNA was categorized by origin, functionality, chromosomal localization and genes, based on public databases (human reference genome build 36.2 and corresponding annotation file seq_gene.md as downloaded from NCBI (ftp.ncbi.nih.gov). The average length of sequenced nucleotides was 185.7 nucleotides and the total number of nucleotides sequenced per sample was 1.2 – 2.6 million. CNA sequences occurring with a frequency significantly greater or less than those observed for healthy controls were evaluated in detail. The next steps were to examine correlations with initial active myeloma, response to treatment, the complete remission state off all therapy, and subsequent relapse. The presence of 10 DNA sequences was highly correlated with the disease course: ZMYM2; TSPAN5; TLL1; PRKD1; ANTXR1; SYT14; PRKCH; MBNL1; EGFR and EDG7. Of these ZYMYM2 was highly correlated with disease reactivation and relapse off therapy. TSPAN5 showed a clear pattern with reduction to background levels during remission, but increase at the very earliest sign of relapse evident on CT-PET. Conversely, other sequences (GRID1; KIF16B) increased substantially during the peak impact of successful therapy. Multivariate analyses were used to identify the best combinations of gene sequences predictive of disease course and outcome. The combination of four genes (GRID1; PRKD1; ANTXR1; GAB1) was sufficient to define the early active disease data points vs the normal controls (odds-ratio OR: 135 [10.6 to 172]; p<.0001). When the resulting model was kept and used as a search engine for the whole 2 years course, the time course followed the treatment success (OR: 54; p=.0017) and failure as well as the final relapse(OR: 13.3; p=.004) In conclusion: Total sequencing of DNA has proved promising in providing personalized molecular monitoring for myeloma. The details of associated DNA sequences provide insights to the underlying molecular pathophysiology linked to myeloma disease progression, response to successful therapy as well as subsequent relapse. Further testing is ongoing.
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Burns, Philip A., Frances L. Allen, and Barry W. Glickman. "DNA SEQUENCE ANALYSIS OF MUTAGENICITY AND SITE SPECIFICITY OF ETHYL METHANESULFONATE IN Uvr+ AND UvrB- STRAINS OF ESCHERICHIA COLI." Genetics 113, no. 4 (August 1, 1986): 811–19. http://dx.doi.org/10.1093/genetics/113.4.811.
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ABSTRACT EMS-induced mutations within a 180 base pair region of the lacI gene of E. coli were cloned and sequenced. In total, 105 and 79 EMS-induced mutations from a Uvr+ and a UvrB- strain, respectively, were sequenced. The specificity of EMS-induced mutagenesis was very similar in the two strians; G:C → A:T transitions accounted for all but three of the mutants. The overall frequency of induced mutation was fivefold higher in the UvrB- strain compared to the Uvr+ strain. This demonstrates, at the DNA sequence level, that the presumed pre-mutagenic lesion, O 6-ethylguanine, is subject to repair by the uvrABC excision repair system of E. coli. An analysis of mutation frequencies with respect to neighboring base sequence, in the two strains, shows that O 6-ethylguanine lesions adjacent to A:T base pairs present better targets for the excision repair machinery than those not adjacent to A:T base pairs.
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Gomes, A. R., S. Vinga, M. Zavolan, and H. de Lencastre. "Analysis of the Genetic Variability of Virulence-Related Loci in Epidemic Clones of Methicillin-Resistant Staphylococcus aureus." Antimicrobial Agents and Chemotherapy 49, no. 1 (January 2005): 366–79. http://dx.doi.org/10.1128/aac.49.1.366-379.2005.
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ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) isolates have previously been classified into major epidemic clonal types by pulsed-field gel electrophoresis in combination with multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec typing. We aimed to investigate whether genetic variability in potentially polymorphic domains of virulence-related factors could provide another level of differentiation in a diverse collection of epidemic MRSA clones. The target regions of strains representative of epidemic clones and genetically related methicillin-susceptible S. aureus isolates from the 1960s that were sequenced included the R domains of clfA and clfB; the D, W, and M regions of fnbA and fnbB; and three regions in the agr operon. Sequence variation ranged from very conserved regions, such as those for RNAIII and the agr interpromoter region, to the highly polymorphic R regions of the clf genes. The sequences of the clf R domains could be grouped into six major sequence types on the basis of the sequences in their 3′ regions. Six sequence types were also observed for the fnb sequences at the amino acid level. From an evolutionary point of view, it was interesting that a small DNA stretch at the 3′ clf R-domain sequence and the fnb sequences agreed with the results of MLST for this set of strains. In particular, clfB R-domain sequences, which had a high discriminatory capacity and with which the types distinguished were congruent with those obtained by other molecular typing methods, have potential for use for the typing of S. aureus. Clone- and strain-specific sequence motifs in the clf and fnb genes may represent useful additions to a typing methodology with a DNA array.
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McAllister, Bryant F., and Gilean A. T. McVean. "Neutral Evolution of the Sex-Determining Gene transformer in Drosophila." Genetics 154, no. 4 (April 1, 2000): 1711–20. http://dx.doi.org/10.1093/genetics/154.4.1711.
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Abstract The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. These changes in amino acid sequence are the result of either natural selection or neutral evolution. To differentiate between selective and neutral causes of this evolutionary change, analyses of both intraspecific and interspecific patterns of molecular evolution of tra gene sequences are presented. Sequences of 31 tra alleles were obtained from Drosophila americana. Many replacement and silent nucleotide variants are present among the alleles; however, the distribution of this sequence variation is consistent with neutral evolution. Sequence evolution was also examined among six species representative of the genus Drosophila. For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. In exon 3 of D. virilis and D. americana we find evidence for an elevated rate of nonsynonymous substitution, but no statistical support for a greater rate of nonsynonymous relative to synonymous substitutions. Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function.
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Hedrick, Philip W., Karen M. Parker, Ellen L. Miller, and Philip S. Miller. "Major Histocompatibility Complex Variation in the Endangered Przewalski’s Horse." Genetics 152, no. 4 (August 1, 1999): 1701–10. http://dx.doi.org/10.1093/genetics/152.4.1701.
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Abstract The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an essential role in recognition of parasites. The Przewalski’s horse is extinct in the wild and all the living individuals descend from 13 founders, most of whom were captured around the turn of the century. One of the primary genetic concerns in endangered species is whether they have ample adaptive variation to respond to novel selective factors. In examining 14 Przewalski’s horses that are broadly representative of the living animals, we found six different class II DRB major histocompatibility sequences. The sequences showed extensive nonsynonymous variation, concentrated in the putative antigen-binding sites, and little synonymous variation. Individuals had from two to four sequences as determined by single-stranded conformation polymorphism (SSCP) analysis. On the basis of the SSCP data, phylogenetic analysis of the nucleotide sequences, and segregation in a family group, we conclude that four of these sequences are from one gene (although one sequence codes for a nonfunctional allele because it contains a stop codon) and two other sequences are from another gene. The position of the stop codon is at the same amino-acid position as in a closely related sequence from the domestic horse. Because other organisms have extensive variation at homologous loci, the Przewalski’s horse may have quite low variation in this important adaptive region.
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Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli, D. R. Grimm, S. M. Hyatt, E. W. Fickus, N. D. Young, and P. B. Cregan. "Single-Nucleotide Polymorphisms in Soybean." Genetics 163, no. 3 (March 1, 2003): 1123–34. http://dx.doi.org/10.1093/genetics/163.3.1123.
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Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.
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Na, J. G., I. Pinto, and M. Hampsey. "Isolation and characterization of SUA5, a novel gene required for normal growth in Saccharomyces cerevisiae." Genetics 131, no. 4 (August 1, 1992): 791–801. http://dx.doi.org/10.1093/genetics/131.4.791.
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Abstract We have identified the sua5 locus as a suppressor of an aberrant ATG codon located in the leader region of the cyc1 gene. The sua5-1 allele enhances the iso-1-cytochrome c steady state level in the cyc1-1019 mutant from 2% to approximately 60% of normal (Cyc+) and also confers a marked slow growth (Slg-) phenotype. Suppression is not a consequence of altered transcription initiation at the cyc1 locus. The SUA5 wild-type gene was isolated and sequenced, revealing an open reading frame (ORF) encoding a potential protein of 46,537 Da. SUA5 transcript analyses were consistent with expression of the predicted ORF and Sua5 antisera detected a protein with an apparent molecular mass of 44 kDa. SUA5 was mapped to chromosome VII, immediately adjacent to the PMR1 gene. Hybridization analysis revealed the presence of a related gene on chromosome XII. Neither the SUA5 DNA sequence nor deduced amino acid sequence showed homology to any sequences in the data banks. Disruption of SUA5 conferred the same Cyc+ and Slg- phenotypes as the sua5-1 suppressor, which is the result of a missense mutation, encoding a Ser107----Phe replacement. In addition, sua5 null mutants lack cytochrome a.a3 and fail to grow on lactate or glycerol medium. These results define SUA5 as a new gene encoding a novel protein that is necessary for normal cell growth.
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Taliercio, Earl, Randy D. Allen, Margaret Essenberg, Natalya Klueva, Henry Nguyen, Mohini A. Patil, Paxton Payton, et al. "Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs." Genome 49, no. 4 (April 1, 2006): 306–19. http://dx.doi.org/10.1139/g05-115.
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In an effort to expand the Gossypium hirsutum L. (cotton) expressed sequence tag (EST) database, ESTs representing a variety of tissues and treatments were sequenced. Assembly of these sequences with ESTs already in the EST database (dbEST, GenBank) identified 9675 cotton sequences not present in GenBank. Statistical analysis of a subset of these ESTs identified genes likely differentially expressed in stems, cotyledons, and drought-stressed tissues. Annotation of the differentially expressed cDNAs tentatively identified genes involved in lignin metabolism, starch biosynthesis and stress response, consistent with pathways likely to be active in the tissues under investigation. Simple sequence repeats (SSRs) were identified among these ESTs, and an inexpensive method was developed to screen genomic DNA for the presence of these SSRs. At least 69 SSRs potentially useful in mapping were identified. Selected amplified SSRs were isolated and sequenced. The sequences corresponded to the EST containing the SSRs, confirming that these SSRs will potentially map the gene represented by the EST. The ESTs containing SSRs were annotated to help identify the genes that may be mapped using these markers.Key words: drought stress, gene annotation, gene mapping, tentative consensus sequence (TC), Xanthomonas campestris.
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Stoltzfus, A., J. F. Leslie, and R. Milkman. "Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB." Genetics 120, no. 2 (October 1, 1988): 345–58. http://dx.doi.org/10.1093/genetics/120.2.345.
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Abstract We present the sequence of a 3500-bp region of the Escherichia coli strain K12 chromosome lying between the tryptophan operon and the tonB gene. Analysis of the sequence yields six open reading frames that have properties characteristic of genes for proteins. The reading frames are closely spaced, and putative transcription units and control sites compose over 95% of the DNA. The sequences of several wild strains of E. coli have been determined for a large segment of the region described. Comparison of these sequences reveals the effects of base substitutions, DNA rearrangements, and recombination. In the regions presumably expressed as polypeptides, most of the natural variation results from synonymous substitutions. However, the DNA rearrangements identified have end points within the open reading frames and disrupt them in a variety of ways. The effects of genetic recombination between strains, recently found to be significant on a large scale in E. coli, are also apparent in the region between trp and tonB.
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Ruiz, Carlos, Diego Cejas, Irene Muñoz, and Pilar De la Rua. "Characterizing the Mitogenome of the Endemic Bumblebee Subspecies from the Canary Islands for Conservation Purposes." Sociobiology 68, no. 3 (August 14, 2021): e5910. http://dx.doi.org/10.13102/sociobiology.v68i3.5910.
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The taxonomic status of Bombus terrestris subspecies is complex and has deep implications in the management of commercial bumblebees for crop pollination as well as in the establishment of appropriate conservation plans. Herein, the complete mitogenome of the endemic Canary Islands subspecies Bombus terrestris canariensis is newly sequenced and compared with available mitochondrial sequences in order to shed light into its taxonomic status. The mitochondrial genome was 17,300 bp in length and contained 37 genes, including 13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs and a partial sequence of the AT rich control region. The phylogenetic analysis of PCGs of the mitogenome was congruent with its subspecific status and a close relationship with the North African subspecies africanus as previously suggested. The sequencing of the mitogenome of B. t. canariensis provides useful genetic information to study the conservation genetics and genetic diversity of these island bumblebee populations.
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Xiong, Yong, Wan Song Yue, Chun Yan Zhao, and Cui Yang. "Amplification and Bioinformatics Analysis of IGS1 Sequence of Aurcularia Auricular." Applied Mechanics and Materials 395-396 (September 2013): 686–90. http://dx.doi.org/10.4028/www.scientific.net/amm.395-396.686.
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The intergenic spacer 1 (IGS1) region in rRNA gene ofAuricularia auriculawas PCR-amplified and sequenced, and the sequence was analyzed by using bioinformatics technology. The two-way sequencing results were spliced by DANMAN software and used MEGA5.10 to analyze sequence variability, calculate genetic distance and construct phylogenetic tree. The amplified fragment length of intergenic spacer 1 (IGS1) gene was about 954bp ~1162bp, GC content of 51.90 to 52.02%, 73 nucleotide variable sites, 16 parsimony informative sites. Variable sites were mainly concentrated in the201~232bp and 714~884bp region. IGS1 sequences have great extent Compared with other 9 species from the GenBank according to the analysis of distance matrix, the genetic relationship between strains and the related known species from systematic dendrogram, IGS1 sequence analysis supports the traditional classification of Auricularia based on morphology. IGS1sequences variation could distinguish the difference between Araucaria species, it could be used as a supplement study genetic diversity method.
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Jordan, I. King, and John F. McDonald. "Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae." Genetics 151, no. 4 (April 1, 1999): 1341–51. http://dx.doi.org/10.1093/genetics/151.4.1341.
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Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.
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Fukasawa, Kayoko M., Masako Tanimura, Ikuya Sakai, Farida S. Sharief, Fu-Zon Chung, and Steven S.-L. Li. "Molecular Nature of Spontaneous Mutations in Mouse Lactate Dehydrogenase-A Processed Pseudogenes." Genetics 115, no. 1 (January 1, 1987): 177–84. http://dx.doi.org/10.1093/genetics/115.1.177.
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ABSTRACT The presence of at least ten mouse LDH-A pseudogenes was demonstrated in the genomic blot analysis, and four different processed pseudogenes have thus far been isolated and characterized. In this report, the nucleotide sequences of two different mouse lactate dehydrogenase-A processed pseudogenes, M11 and M14, were determined and compared with the protein-coding sequences of the mouse and rat LDH-A functional genes. In the pseudogene M11, the sequence of 64 nucleotides from codon no. 257 to 278 was tandemly duplicated. In the pseudogene M14, the sequence of 22 nucleotides from codon no. 68 to 75 was replaced by an inserted repetitive sequence of 242 nucleotides homologous to a mouse truncated R element. The pattern of nucleotide substitutions accumulated in mouse LDH-A pseudogenes M11 and M14, as well as that of pseudogene M10 identified previously, was analyzed, and the substitution frequencies of the C or G at the CG dinucleotide were found to be high.
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Xiang, Niyan, Bojie Lu, Tao Yuan, Tiange Yang, Jiani Guo, Zhihua Wu, Hong Liu, Xing Liu, and Rui Qin. "De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum." Genes 14, no. 2 (January 21, 2023): 279. http://dx.doi.org/10.3390/genes14020279.
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Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Lilly, Jason W., and Michael J. Havey. "Small, Repetitive DNAs Contribute Significantly to the Expanded Mitochondrial Genome of Cucumber." Genetics 159, no. 1 (September 1, 2001): 317–28. http://dx.doi.org/10.1093/genetics/159.1.317.
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Abstract Closely related cucurbit species possess eightfold differences in the sizes of their mitochondrial genomes. We cloned mitochondrial DNA (mtDNA) fragments showing strong hybridization signals to cucumber mtDNA and little or no signal to watermelon mtDNA. The cucumber mtDNA clones carried short (30–53 bp), repetitive DNA motifs that were often degenerate, overlapping, and showed no homology to any sequences currently in the databases. On the basis of dot-blot hybridizations, seven repetitive DNA motifs accounted for >13% (194 kb) of the cucumber mitochondrial genome, equaling >50% of the size of the Arabidopsis mitochondrial genome. Sequence analysis of 136 kb of cucumber mtDNA revealed only 11.2% with significant homology to previously characterized mitochondrial sequences, 2.4% to chloroplast DNA, and 15% to the seven repetitive DNA motifs. The remaining 71.4% of the sequence was unique to the cucumber mitochondrial genome. There was <4% sequence colinearity surrounding the watermelon and cucumber atp9 coding regions, and the much smaller watermelon mitochondrial genome possessed no significant amounts of cucumber repetitive DNAs. Our results demonstrate that the expanded cucumber mitochondrial genome is in part due to extensive duplication of short repetitive sequences, possibly by recombination and/or replication slippage.
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Szopa, J. "Expression analysis of a Cucurbita cDNA encoding endonuclease." Acta Biochimica Polonica 42, no. 2 (June 30, 1995): 183–89. http://dx.doi.org/10.18388/abp.1995_4643.
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The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3 protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber.
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Nachman, M. W., S. N. Boyer, J. B. Searle, and C. F. Aquadro. "Mitochondrial DNA variation and the evolution of Robertsonian chromosomal races of house mice, Mus domesticus." Genetics 136, no. 3 (March 1, 1994): 1105–20. http://dx.doi.org/10.1093/genetics/136.3.1105.
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Abstract The house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races with diploid numbers from 2n = 22 to 2n = 38. Although these races are highly differentiated karyotypically, they are otherwise indistinguishable from standard karyotype (i.e., 2n = 40) mice, and consequently their evolutionary histories are not well understood. We have examined mitochondrial DNA (mtDNA) sequence variation from the control region and the ND3 gene region among 56 M. domesticus from Western Europe, including 15 Rb populations and 13 standard karyotype populations, and two individuals of the sister species, Mus musculus. mtDNA exhibited an average sequence divergence of 0.84% within M. domesticus and 3.4% between M. domesticus and M. musculus. The transition/transversion bias for the regions sequenced is 5.7:1, and the overall rate of sequence evolution is approximately 10% divergence per million years. The amount of mtDNA variation was as great among different Rb races as among different populations of standard karyotype mice, suggesting that different Rb races do not derive from a single recent maternal lineage. Phylogenetic analysis of the mtDNA sequences resulted in a parsimony tree which contained six major clades. Each of these clades contained both Rb and standard karyotype mice, consistent with the hypothesis that Rb races have arisen independently multiple times. Discordance between phylogeny and geography was attributable to ancestral polymorphism as a consequence of the recent colonization of Western Europe by mice. Two major mtDNA lineages were geographically localized and contained both Rb and standard karyotype mice. The age of these lineages suggests that mice have moved into Europe only within the last 10,000 years and that Rb populations in different geographic regions arose during this time.
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Ahmad, Awais, Xin Yang, Ting Zhang, Chunqun Wang, Caixian Zhou, Xingrun Yan, Mubashar Hassan, Muhammad Ikram, and Min Hu. "Characterization of the Complete Mitochondrial Genome of Ostertagia trifurcata of Small Ruminants and its Phylogenetic Associations for the Trichostrongyloidea Superfamily." Genes 10, no. 2 (January 31, 2019): 107. http://dx.doi.org/10.3390/genes10020107.
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The complete mitochondrial (mt) genome of Ostertagia trifurcata, a parasitic nematode of small ruminants, has been sequenced and its phylogenetic relationship with selected members from the superfamily Trichostrongyloidea was investigated on the basis of deduced datasets of mt amino acid sequences. The entire mt genome of Ostertagia trifurcata is circular and 14,151 bp in length. It consists of a total of 36 genes comprising 12 genes coding for proteins (PCGs), 2 genes for ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes and 2 non-coding regions, since all genes are transcribed in the same direction. The phylogenetic analysis based on the concatenated datasets of predicted amino acid sequences of the 12 protein coding genes supported monophylies of the Haemonchidae, Dictyocaulidae and Molineidae families, but rejected monophylies of the Trichostrongylidae family. The complete characterization and provision of the mtDNA sequence of Ostertagia trifurcata provides novel genetic markers for molecular epidemiological investigations, systematics, diagnostics and population genetics of Ostertagia trifurcata and its correspondents.
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Gorbunova, Vera, and Avraham A. Levy. "Analysis of Extrachromosomal Ac/Ds Transposable Elements." Genetics 155, no. 1 (May 1, 2000): 349–59. http://dx.doi.org/10.1093/genetics/155.1.349.
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Abstract The mechanism of transposition of the maize Ac/Ds elements is not well understood. The true transposition intermediates are not known and it has not been possible to distinguish between excision models involving 8-bp staggered cuts or 1-bp staggered cuts followed by hairpin formation. In this work, we have analyzed extrachromosomal excision products to gain insight into the excision mechanism. Plasmid rescue was used to demonstrate that Ds excision is associated with the formation of circular molecules. In addition, we present evidence for the formation of linear extrachromosomal species during Ds excision. Sequences found at the termini of circular and linear elements showed a broad range of nucleotide additions or deletions, suggesting that these species are not true intermediates. Additional nucleotides adjacent to the termini in extrachromosomal elements were compared to the sequence of the original donor site. This analysis showed that: (1) the first nucleotide adjacent to the transposon end was significantly more similar to the first nucleotide flanking the element in the donor site than to a random sequence and (2) the second and farther nucleotides did not resemble the donor site. The implications of these findings for excision models are discussed.
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Coyne, Robert S., and Meng-Chao Yao. "Evolutionary Conservation of Sequences Directing Chromosome Breakage and rDNA Palindrome Formation in Tetrahymenine Ciliates." Genetics 144, no. 4 (December 1, 1996): 1479–87. http://dx.doi.org/10.1093/genetics/144.4.1479.
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Extensive, programmed chromosome breakage occurs during formation of the somatic macronucleus of ciliated protozoa. The cis-acting signal directing breakage has been most rigorously defined in Tetrahymena thermophila, where it consists of a 15-bp DNA sequence known as Cbs, for chromosome breakage sequence. We have identified sequences identical or nearly identical to the T. thermophila Cbs at sites of breakage flanking the germline micronuclear rDNA locus of six additional species of Tetrahymena as well as members of two related genera. Other general features of the breakage site are also conserved, but surprisingly, the orientation and number of copies of Cbs are not always conserved, suggesting the occurrence of germline rearrangement events over evolutionary time. At one end of the T. thermophila micronuclear rDNA locus, a pair of short inverted repeats adjacent to Cbs directs the formation of a giant palindromic molecule. We have examined the corresponding sequences from two other Tetrahymena species. We find the sequence to be partially conserved, as previously implied from analysis of macronuclear rDNA, but of variable length and organization.