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1
Kami, James A., and Paul Gepts. "Phaseolin nucleotide sequence diversity in Phaseolus. I. Intraspecific diversity in Phaseolus vulgaris." Genome 37, no. 5 (October 1, 1994): 751–57. http://dx.doi.org/10.1139/g94-107.
Повний текст джерелаАнотація:
Most information about the molecular biology of phaseolin, the major seed storage protein in Phaseolus vulgaris, has been obtained from the T-type phaseolin, which is characteristic of the Andean gene pool of the species. In the work reported here, two cDNA clones for the S-type phaseolin representing the other major, Middle American gene pool were isolated and sequenced. Analysis of the DNA sequences revealed the presence of two subtypes of S phaseolin, α and β, depending on the presence or absence, respectively, of a 27-bp direct repeat. These are similar to the α- and β-phaseolin subtypes found in the Andean, T phaseolin; however, the additional 15-bp direct repeat also found in the T α-phaseolin gene type was apparently absent from the S α-phaseolin genes. The overall sequence identity was greater between the α or β subtypes of different gene pools than between the a or p subtypes within gene pools. This implies that the gene subtypes were formed prior to the formation of the two major gene pools of P. vulgaris. Analysis of the putative amino acid sequence revealed that both the 'Sanilac' phaseolin subtypes contained an additional methionine, however, not at the same site. This opens the possibility of increasing the nutritionally limiting methionine level in phaseolin either through protein engineering or by screening accessions for recombinant phaseolin sequences that combine both substitutions.Key words: seed storage protein, multigene family, direct repeat.
2
Suerbaum, Sebastian, Marc Lohrengel, Agnes Sonnevend, Florian Ruberg, and Manfred Kist. "Allelic Diversity and Recombination inCampylobacter jejuni." Journal of Bacteriology 183, no. 8 (April 15, 2001): 2553–59. http://dx.doi.org/10.1128/jb.183.8.2553-2559.2001.
Повний текст джерелаАнотація:
ABSTRACT The allelic diversity and population structure ofCampylobacter jejuni were studied by multilocus nucleotide sequence analysis. Sequences from seven housekeeping genes were obtained from 32 C. jejuni isolates isolated from enteritis patients in Germany, Hungary, Thailand, and the United States. Also included was strain NCTC 11168, the complete genomic sequence of which has recently been published. For all loci analyzed, multiple strains carried identical alleles. The frequency of synonymous and nonsynonymous sequence polymorphisms was low. The number of unique alleles per locus ranged from 9 to 15. These alleles occurred in 31 different combinations (sequence types), so that all but two pairs of strains could be distinguished from each other. Sequences were analyzed for evidence of recombination by the homoplasy test and split decomposition. These analyses showed that intraspecific recombination is frequent in C. jejuni and has generated extensive diversity of allelic profiles from a small number of polymorphic nucleotides.
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Garcia Machado, Erik, Mario Oliva Suarez, Nicole Dennebouy, Monique Monnerot, and Jean-Claude Mounolou. "Mitochondrial 16S-rRna Gene of Two Species of Shrimps: Sequence Variability and Secondary Structure." Crustaceana 65, no. 3 (1993): 279–86. http://dx.doi.org/10.1163/156854093x00711.
Повний текст джерелаАнотація:
AbstractPart of the mitochondrial 16S-ribosomal RNA gene (around 400 nucleotides) of Penaeus notialis and Penaeus schmitti has been amplified and sequenced. The comparison of sequences reveals an 11% nucleotide divergence between the two species. When compared with that of the homologous fragment in Artemia salina and Drosophila yakuba, the secondary structure appears well conserved in spite of high nucleotide divergence due to numerous substitutions and additions/deletions. Sequences have been obtained for six individuals of P. notialis belonging to the same population, their comparison shows a 0.7% nucleotide diversity.
4
Geering, A. D. W., L. A. McMichael, R. G. Dietzgen, and J. E. Thomas. "Genetic Diversity Among Banana streak virus Isolates from Australia." Phytopathology® 90, no. 8 (August 2000): 921–27. http://dx.doi.org/10.1094/phyto.2000.90.8.921.
Повний текст джерелаАнотація:
Banana streak virus (BSV) is an important pathogen of bananas and plantains (Musa spp.) throughout the world. We have cloned and sequenced part of the genomes of four isolates of BSV from Australia, designated BSV-RD, BSV-Cav, BSV-Mys, and BSV-GF. These isolates originated from banana cvs. Red Dacca, Williams, Mysore, and Goldfinger, respectively. All clones contained a sequence covering part of open reading frame III and the intergenic region of the badnavirus genome. The sequences were compared with those of other badnaviruses, including BSV-Onne, a previously characterized isolate from Nigeria. The BSV-RD sequence was virtually identical to that of BSV-Onne, differing by only two nucleotides over 1,292 bp. However, BSV-Cav, -Mys, and -GF were divergent in nucleotide sequence. Phylogenetic analyses using conserved sequences in the ribonuclease H domain revealed that all BSV isolates were more closely related to each other than to any other badnavirus. BSV-Cav was most closely related to BSV-Onne, and there was 95.1% identity between the two amino acid sequences. Other relationships between the BSV isolates were less similar, with sequence identities ranging from 66.4 to 78.2%, which is a magnitude comparable to the distance between some of the recognized badnavirus species. Immunocapture-polymerase chain reaction assays have been developed, allowing specific detection and differentiation of the four isolates of BSV.
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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.
Повний текст джерелаАнотація:
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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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.
Повний текст джерелаАнотація:
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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Ren, Xifeng, Yonggang Wang, Songxian Yan, Dongfa Sun, and Genlou Sun. "Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley." Genome 57, no. 4 (April 2014): 239–44. http://dx.doi.org/10.1139/gen-2014-0039.
Повний текст джерелаАнотація:
Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.
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Zhang, Nian-Zhang, Ying Xu, Si-Yang Huang, Dong-Hui Zhou, Rui-Ai Wang, and Xing-Quan Zhu. "Sequence Variation inToxoplasma gondii rop17Gene among Strains from Different Hosts and Geographical Locations." Scientific World Journal 2014 (2014): 1–4. http://dx.doi.org/10.1155/2014/349325.
Повний текст джерелаАнотація:
Genetic diversity ofT. gondiiis a concern of many studies, due to the biological and epidemiological diversity of this parasite. The present study examined sequence variation in rhoptry protein 17 (ROP17) gene amongT. gondiiisolates from different hosts and geographical regions. Therop17gene was amplified and sequenced from 10T. gondiistrains, and phylogenetic relationship among theseT. gondiistrains was reconstructed using maximum parsimony (MP), neighbor-joining (NJ), and maximum likelihood (ML) analyses. The partialrop17gene sequences were 1375 bp in length and A+T contents varied from 49.45% to 50.11% among all examinedT. gondiistrains. Sequence analysis identified 33 variable nucleotide positions (2.1%), 16 of which were identified as transitions. Phylogeny reconstruction based onrop17gene data revealed two major clusters which could readily distinguish Type I and Type II strains. Analyses of sequence variations in nucleotides and amino acids among these strains revealed high ratio of nonsynonymous to synonymous polymorphisms (>1), indicating thatrop17shows signs of positive selection. This study demonstrated the existence of slightly high sequence variability in therop17gene sequences amongT. gondiistrains from different hosts and geographical regions, suggesting thatrop17gene may represent a new genetic marker for population genetic studies ofT. gondiiisolates.
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Raphael, Brian H., Mallory J. Choudoir, Carolina Lúquez, Rafael Fernández, and Susan E. Maslanka. "Sequence Diversity of Genes Encoding Botulinum Neurotoxin Type F." Applied and Environmental Microbiology 76, no. 14 (May 28, 2010): 4805–12. http://dx.doi.org/10.1128/aem.03109-09.
Повний текст джерелаАнотація:
ABSTRACT Botulism due to type F botulinum neurotoxin (BoNT/F) is rare (<1% of cases), and only a limited number of clostridial strains producing this toxin type have been isolated. As a result, analysis of the diversity of genes encoding BoNT/F has been challenging. In this study, the entire bont/F nucleotide sequences were determined from 33 type F botulinum toxin-producing clostridial strains isolated from environmental sources and botulism outbreak investigations. We examined proteolytic and nonproteolytic Clostridium botulinum type F strains, bivalent strains, including Bf and Af, and Clostridium baratii type F strains. Phylogenetic analysis revealed that the bont/F genes examined formed 7 subtypes (F1 to F7) and that the nucleotide sequence identities of these subtypes differed by up to 25%. The genes from proteolytic (group I) C. botulinum strains formed subtypes F1 through F5, while the genes from nonproteolytic (group II) C. botulinum strains formed subtype F6. Subtype F7 was composed exclusively of bont/F genes from C. baratii strains. The region of the bont/F5 gene encoding the neurotoxin light chain was found to be highly divergent compared to the other subtypes. Although the bont/F5 nucleotide sequences were found to be identical in strains harboring this gene, the gene located directly upstream (ntnh/F) demonstrated sequence variation among representative strains of this subtype. These results demonstrate that extensive nucleotide diversity exists among genes encoding type F neurotoxins from strains with different phylogenetic backgrounds and from various geographical sources.
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Ali, Shaymaa H., Jaladet M. S. Jubrael, and Caroline Bowsher. "Genetic diversity and nucleotide sequence analysis of powdery mildew marker and Vf2RAD resistant gene in apple (Malus domestica) land races." Innovaciencia Facultad de Ciencias Exactas, Físicas y Naturales 6, no. 1 (December 28, 2018): 1–10. http://dx.doi.org/10.15649/2346075x.460.
Повний текст джерелаАнотація:
Introduction: DNA sequencing-based methods and nucleotide sequence analysis have become the most common molecular approaches currently used for molecular typing purposes and phylogenetic diversity analysis. Methods: In this study, the nucleotide sequence variations of Powdery mildew resistance gene marker (CH03c02) and the apple scab resistance gene (Vf2RAD) beside phylogenetic diversity of seven apple landraces have been investigated. The two-locus have been successfully cloned and their nucleotide sequences were determined across all studied landraces. Results: Results of sequence alignment of the Powdery mildew resistant locus (CH03c02), compared with that of the published sequence of the same locus of Discovery genotype (HiDRAS), revealed that the nucleotide variations of this locus ranged from 1 to 28 nucleotide substitutions across all seven apple landraces. Whilst, the nucleotide variations of VF2RAD ranged from 2-8 nucleotide substitutions across all the investigated landraces. The highest genetic distance (0.062) was between Amara and Barwari. Whereas, the lowest genetic distance (0.0015) was found between each of the Lubnani, Rechard, Ispartal, and the Ahmadagha. The nucleotide sequences of the two loci were concatenated and implemented to build a Neighbor-Joining tree. The seven apple landraces were successfully grouped into two main genetic clusters (C1 and C2) in the phylogenetic tree. Conclusions: It can be concluded that the cloning approach used in the current study was found to be very successful and helpful for obtaining the full nucleotide sequences of these two loci. The investigated loci were displayed nucleotide variations among the studied landraces. And, finding of these variations was allowed the distinguishing and discrimination of these landraces.
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Servant, Annabelle, Syria Laperche, Francis Lallemand, Valérie Marinho, Guillemette De Saint Maur, Jean François Meritet, and Antoine Garbarg-Chenon. "Genetic Diversity within Human Erythroviruses: Identification of Three Genotypes." Journal of Virology 76, no. 18 (September 15, 2002): 9124–34. http://dx.doi.org/10.1128/jvi.76.18.9124-9134.2002.
Повний текст джерелаАнотація:
ABSTRACT B19 virus is a human virus belonging to the genus Erythrovirus. The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of B19 virus. To date, the V9 isolate remains the unique representative of a new variant in the genus Erythrovirus, and its taxonomic position is unclear. We report here the isolation of 11 V9-related viruses. A prospective study conducted in France between 1999 and 2001 indicates that V9-related viruses actually circulate at a significant frequency (11.4%) along with B19 viruses. Analysis of the nearly full-length genome sequence of one V9-related isolate (D91.1) indicates that the D91.1 sequence clusters together with but is notably distant from the V9 sequence (5.3% divergence) and is distantly related to B19 virus sequences (13.8 to 14.2% divergence). Additional phylogenetic analysis of partial sequences from the V9-related isolates combined with erythrovirus sequences available in GenBank indicates that the erythrovirus group is more diverse than thought previously and can be divided into three well-individualized genotypes, with B19 viruses corresponding to genotype 1 and V9-related viruses being distributed into genotypes 2 and 3.
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Welsh, Allana K., Jeffrey O. Dawson, Gerald J. Gottfried, and Dittmar Hahn. "Diversity of Frankia Populations in Root Nodules of Geographically Isolated Arizona Alder Trees in Central Arizona (United States)." Applied and Environmental Microbiology 75, no. 21 (September 4, 2009): 6913–18. http://dx.doi.org/10.1128/aem.01103-09.
Повний текст джерелаАнотація:
ABSTRACT The diversity of uncultured Frankia populations in root nodules of Alnus oblongifolia trees geographically isolated on mountaintops of central Arizona was analyzed by comparative sequence analyses of nifH gene fragments. Sequences were retrieved from Frankia populations in nodules of four trees from each of three mountaintops (n = 162) and their levels of diversity compared using spatial genetic clustering methods and single-nucleotide or 1, 3, or 5% sequence divergence thresholds. With the single-nucleotide threshold level, 45 different sequences with significant differences between the mountaintops were retrieved, with the southern site partitioning in a separate population from the two other sites. Some of these sequences were identical in nodules from different mountaintops and to those of strains isolated from around the world. A high level of diversity that resulted in the assignment of 14 clusters of sequences was also found on the 1% divergence level. Single-nucleotide and 1% divergence levels thus demonstrate microdiversity of frankiae in root nodules of A. oblongifolia trees and suggest a partitioning of diversity by site. At the 3 and 5% divergence levels, however, diversity was reduced to three clusters or one cluster, respectively, with no differentiation by mountaintop. Only at the 5% threshold level do all Frankia strains previously assigned to one genomic group cluster together.
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Rwegasira, G. M., G. Momanyi, M. E. C. Rey, G. Kahwa, and J. P. Legg. "Widespread Occurrence and Diversity of Cassava brown streak virus (Potyviridae: Ipomovirus) in Tanzania." Phytopathology® 101, no. 10 (October 2011): 1159–67. http://dx.doi.org/10.1094/phyto-11-10-0297.
Повний текст джерелаАнотація:
Cassava brown streak disease (CBSD) has been a problem in Tanzania since 1936. Existing literature indicated limited distribution of the disease to low altitudes, usually <100 m above sea level, but the current geographical distribution of the disease was not known. Whether a single or many strains for the virus exist in Tanzania had not been reported to date. In this study, CBSD was recorded from sea level to ≈1,800 m above sea level. In total, 2,730 cassava plants were assessed for CBSD leaf symptoms in 91 fields and root symptoms were assessed at 81 sites. A sample was taken from each site for laboratory screening for Cassava brown streak virus (CBSV). CBSD mean foliar and root incidences were 38 and 36%, respectively. Reverse-transcription polymerase chain reaction of a partial 3′-terminal coat protein (CP) region of CBSV indicated the presence of CBSV in 67 of the 91 (73%) samples. Forty-three amplicons were sequenced, and phylogenetic comparisons with nucleotide sequences from GenBank (National Center for Biotechnology Information database) suggested that one major clade of CBSV primarily exists in Tanzania. However, there was nucleotide sequence divergence of up to 19% among the 42 isolates. In all, 42 of the 43 sequences had 80 to 100% nucleotide identity with 6 previously reported CP-CBSV sequences (from Mozambique and Tanzania). In total, 13 of 42 isolates had <80% nucleotide identities with three previously reported Ugandan CBSV sequences. One isolate, FJ687177, shared <78% sequence identity with the other Tanzanian sequences but was closely related (93%) to Ugandan isolates. It is likely that isolate FJ687177 may belong to a less widely distributed recently described species (clade 2) of CBSV, named Ugandan cassava brown streak virus (UCBSV).
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Fudyk, Trevor C., Ian W. Maclean, J. Neil Simonsen, Ephantus N. Njagi, Joshua Kimani, Robert C. Brunham, and Francis A. Plummer. "Genetic Diversity and Mosaicism at the por Locus ofNeisseria gonorrhoeae." Journal of Bacteriology 181, no. 18 (September 15, 1999): 5591–99. http://dx.doi.org/10.1128/jb.181.18.5591-5599.1999.
Повний текст джерелаАнотація:
ABSTRACT The por genes of the predominant serovars ofNeisseria gonorrhoeae circulating in a high-frequency transmitter core group located in Nairobi, Kenya, were examined for nucleotide sequence polymorphism. The level of por gene diversity did not differ significantly between core group-derived gonococcal strains and gonococcal strains originating elsewhere. However, por mosaicism appeared to be more frequent among core group-derived strains, suggesting that recombination of differentpor sequences may be a important strategy by which N. gonorrhoeae generates por gene diversity within core group populations. Despite extensive sequence variability,por expressed by gonococcal isolates of different geographic origin exhibited conserved patterns of nucleotide change, suggesting that diversity among por alleles may also be finite.
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Lin, Jing-Zhong, Peter L. Morrell, and Michael T. Clegg. "The Influence of Linkage and Inbreeding on Patterns of Nucleotide Sequence Diversity at Duplicate Alcohol Dehydrogenase Loci in Wild Barley (Hordeum vulgaressp. spontaneum)." Genetics 162, no. 4 (December 1, 2002): 2007–15. http://dx.doi.org/10.1093/genetics/162.4.2007.
Повний текст джерелаАнотація:
AbstractPatterns of nucleotide sequence diversity are analyzed for three duplicate alcohol dehydrogenase loci (adh1-adh3) within a species-wide sample of 25 accessions of wild barley (Hordeum vulgare ssp. spontaneum). The adh1 and adh2 loci are tightly linked (recombination fraction <0.01) while the adh3 locus is inherited independently. Wild barley is predominantly self-fertilizing (∼98%), and as a consequence, effective recombination is restricted by the extreme reduction in heterozygosity. Large reductions in effective recombination, in turn, widen the conditions for linkage to influence nucleotide sequence diversity through the action of selective sweeps or background selection. These considerations would appear to predict (1) homogeneity in patterns of nucleotide sequence diversity, especially between closely linked loci, and (2) extensive linkage disequilibrium relative to random-mating species. In contrast to these expectations, the wild barley data reveal heterogeneity in patterns of nucleotide sequence diversity and levels of linkage disequilibrium that are indistinguishable from those observed at adh1 in maize, an outbreeding grass species.
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Kaartinen, M., and O. Mäkelä. "Functional analogues of the VKOx1 gene in different strains of mice: evolutionary conservation but diversity based on V-J joining." Journal of Immunology 138, no. 5 (March 1, 1987): 1613–17. http://dx.doi.org/10.4049/jimmunol.138.5.1613.
Повний текст джерелаАнотація:
Abstract Monoclonal antibodies to the hapten phenyloxazolone were raised 7 days after immunization in mice of six strains (BALB/c, C57BL-Igha, DBA2, RF, A/J, and CE). Hybridomas were selected that produced 260 idiotype-positive antibodies, and their light chain mRNA were partially sequenced. (RF is an idiotype-negative strain, and sequencing was done without this selection.) All newly sequenced BALB/c, C57BL-Igha, DBA/2, A/J, or CE VK segments had a 100% nucleotide homology with the VKOx1 (H3) germline gene. This gene codes for one third of early BALB/c phenyloxazolone antibodies, and according to our results the same gene has a significant role in the early response of at least five strains of mice. Four RF hybridomas had identical nucleotide sequences, suggesting that they express a non-mutated nucleotide sequence of a new VK germ-line gene (VKOx2). This gene codes for a CDR1 which is two amino acids longer than the CDR1 coded by the VKOx1 gene, but otherwise the two genes are related (94.5% sequence homology). All but one of the 16 kappa chains studied had the J5 segment; this segment had the same sequence in all six strains. One RF antibody had the J4 segment the nucleotide sequence of which differs from the BALB/c J4 segment in two places. Three of the kappa chains had an extra long CDR3. Long and "normal" kappa chains were probably coded by the same pair of germ-line genes (VKOx1 and J5, or VKOx2 and J5). The length heterogeneity was probably caused by a lack of precision in VK-JK joining.
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Lúquez, Carolina, Brian H. Raphael, and Susan E. Maslanka. "Neurotoxin Gene Clusters in Clostridium botulinum Type Ab Strains." Applied and Environmental Microbiology 75, no. 19 (August 14, 2009): 6094–101. http://dx.doi.org/10.1128/aem.01009-09.
Повний текст джерелаАнотація:
ABSTRACT There is limited knowledge of the neurotoxin gene diversity among Clostridium botulinum type Ab strains. Only the sequences of the bont/A and bont/B genes in C. botulinum type Ab strain CDC1436 and the sequence of the bont/B gene in C. botulinum type Ab strain CDC588 have been reported. In this study, we sequenced the entire bont/A- and bont/B-associated neurotoxin gene clusters of C. botulinum type Ab strain CDC41370 and the bont/A gene of strain CDC588. In addition, we analyzed the organization of the neurotoxin gene clusters in strains CDC588 and CDC1436. The bont/A nucleotide sequence of strain CDC41370 differed from those of the known bont/A subtypes A1 to A4 by 2 to 7%, and the predicted amino acid sequence differed by 4% to 14%. The bont/B nucleotide sequence in strain CDC41370 showed 99.7% identity to the sequence of subtype B1. The bont/A nucleotide sequence of strain CDC588 was 99.9% identical to that of subtype A1. Although all of the C. botulinum type Ab strains analyzed contained the two sets of neurotoxin clusters, similar to what has been found in other bivalent strains, the intergenic spacing of p21-orfX1 and orfX2-orfX3 varied among these strains. The type Ab strains examined in this study had differences in their toxin gene cluster compositions and bont/A and bont /B nucleotide sequences, suggesting that they may have arisen from separate recombination events.
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Geliebter, J., and S. G. Nathenson. "Microrecombinations generate sequence diversity in the murine major histocompatibility complex: analysis of the Kbm3, Kbm4, Kbm10, and Kbm11 mutants." Molecular and Cellular Biology 8, no. 10 (October 1988): 4342–52. http://dx.doi.org/10.1128/mcb.8.10.4342-4352.1988.
Повний текст джерелаАнотація:
The mechanism that generates spontaneous mutants of the Kb histocompatibility gene was analyzed. Nucleotide sequence analysis of four mutant genes (Kbm3, Kbm4, Kbm10, and Kbm11) revealed that each mutant K gene contains clustered, multiple nucleotide substitutions. Hybridization analyses of parental B6 genomic DNA and cloned class I genes with mutant-specific oligonucleotide probes, followed by sequence analyses, have identified major histocompatibility complex class I genes in the K, D, and Tla regions (K1, Db, and T5, respectively) that contain the exact sequences as substituted into mutant Kb genes. These data provide evidence for the hypothesis that the mutant Kb genes are generated by a microrecombination (gene conversion) mechanism that results in the transfer of small DNA segments from class I genes of all four regions of the major histocompatibility complex (K, D, Qa, and Tla) to Kb. Many of the nucleotides substituted into the mutant Kb genes were identical to those found in other naturally occurring K alleles such as Kd. Thus, we propose that the accumulation of microrecombination products within the K genes of a mouse population is responsible for the high sequence diversity among H-2 alleles.
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Geliebter, J., and S. G. Nathenson. "Microrecombinations generate sequence diversity in the murine major histocompatibility complex: analysis of the Kbm3, Kbm4, Kbm10, and Kbm11 mutants." Molecular and Cellular Biology 8, no. 10 (October 1988): 4342–52. http://dx.doi.org/10.1128/mcb.8.10.4342.
Повний текст джерелаАнотація:
The mechanism that generates spontaneous mutants of the Kb histocompatibility gene was analyzed. Nucleotide sequence analysis of four mutant genes (Kbm3, Kbm4, Kbm10, and Kbm11) revealed that each mutant K gene contains clustered, multiple nucleotide substitutions. Hybridization analyses of parental B6 genomic DNA and cloned class I genes with mutant-specific oligonucleotide probes, followed by sequence analyses, have identified major histocompatibility complex class I genes in the K, D, and Tla regions (K1, Db, and T5, respectively) that contain the exact sequences as substituted into mutant Kb genes. These data provide evidence for the hypothesis that the mutant Kb genes are generated by a microrecombination (gene conversion) mechanism that results in the transfer of small DNA segments from class I genes of all four regions of the major histocompatibility complex (K, D, Qa, and Tla) to Kb. Many of the nucleotides substituted into the mutant Kb genes were identical to those found in other naturally occurring K alleles such as Kd. Thus, we propose that the accumulation of microrecombination products within the K genes of a mouse population is responsible for the high sequence diversity among H-2 alleles.
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Ferguson, S. E., S. Rudikoff, and B. A. Osborne. "Interaction and sequence diversity among T15 VH genes in CBA/J mice." Journal of Experimental Medicine 168, no. 4 (October 1, 1988): 1339–49. http://dx.doi.org/10.1084/jem.168.4.1339.
Повний текст джерелаАнотація:
Nucleotide sequences of the four genes composing the T15 heavy chain variable region (VH) family of the CBA/J mouse have been determined. Comparison of these sequences with their published BALB/c and C57BL/10 homologues reveals that nucleotide differences found between given alleles of two strains, i.e., CBA/J and BALB/c, are observed in other family members of the same strain. We suggest that these patterns of sequence variation are most readily explained by gene interaction (conversion). Additionally, the sequence of a CBA/J hybridoma, 6G6, proposed to have been generated by gene conversion, is directly encoded by the CBA/J V11 gene indicating that the putative conversion has occurred meiotically in the germline. These results are consistent with the premise that gene correction is occurring frequently among members of this family and that such processes may contribute significantly to the evolution of Ig variable region genes even in the relatively short time frame of inbred strain derivation.
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Huebner, Rebeca, Robert Mugabi, Gabriella Hetesy, Lawrence Fox, Sarne De Vliegher, Anneleen De Visscher, John W. Barlow, and George Sensabaugh. "Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence typing." PLOS ONE 16, no. 3 (March 15, 2021): e0243688. http://dx.doi.org/10.1371/journal.pone.0243688.
Повний текст джерелаАнотація:
Staphylococcus chromogenes is a common skin commensal in cattle and has been identified as a frequent cause of bovine mastitis and intramammary infections. We have developed a seven locus Multilocus Sequence Typing (MLST) scheme for typing S. chromogenes. Sequence-based typing systems, such as MLST, have application in studies of genetic diversity, population structure, and epidemiology, including studies of strain variation as a factor in pathogenicity or host adaptation. The S. chromogenes scheme was tested on 120 isolates collected from three geographic locations, Vermont and Washington State in the United States and Belgium. A total of 46 sequence types (STs) were identified with most of the STs being location specific. The utility of the typing scheme is indicated by a discrimination power of 95.6% for all isolates and greater than 90% for isolates from each of the three locations. Phylogenetic analysis placed 39 of the 46 STs into single core group consistent with a common genetic lineage; the STs in this group differ by less than 0.5% at the nucleotide sequence level. Most of the diversification in this lineage group can be attributed to mutation; recombination plays a limited role. This lineage group includes two clusters of single nucleotide variants in starburst configurations indicative of recent clonal expansion; nearly 50% of the isolates sampled in this study are in these two clusters. The remaining seven STs were set apart from the core group by having alleles with highly variable sequences at one or more loci. Recombination had a higher impact than mutation in the diversification of these outlier STs. Alleles with hypervariable sequences were detected at five of the seven loci used in the MLST scheme; the average sequence distances between the hypervariable alleles and the common core alleles ranged from 12 to 34 nucleotides. The extent of these sequence differences suggests the hypervariable alleles may be remnants of an ancestral genotype.
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Innan, Hideki, Ryohei Terauchi, Günter Kahl, and Fumio Tajima. "A Method for Estimating Nucleotide Diversity From AFLP Data." Genetics 151, no. 3 (March 1, 1999): 1157–64. http://dx.doi.org/10.1093/genetics/151.3.1157.
Повний текст джерелаАнотація:
Abstract A method for estimating the nucleotide diversity from AFLP data is developed by using the relationship between the number of nucleotide changes and the proportion of shared bands. The estimation equation is based on the assumption that GC-content is 0.5. Computer simulations, however, show that this method gives a reasonably accurate estimate even when GC-content deviates from 0.5, as long as the number of nucleotide changes per site (nucleotide diversity) is small. As an example, the nucleotide diversity of the wild yam, Dioscorea tokoro, was estimated. The estimated nucleotide diversity is 0.0055, which is larger than estimations from nucleotide sequence data for Adh and Pgi.
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Parthasarathi, Balasamudram Chandrasekhar, Binod Kumar, Gaurav Nagar, Haranahally Vasanthachar Manjunathachar, José de la Fuente, and Srikant Ghosh. "Analysis of Genetic Diversity in Indian Isolates of Rhipicephalus microplus Based on Bm86 Gene Sequence." Vaccines 9, no. 3 (February 26, 2021): 194. http://dx.doi.org/10.3390/vaccines9030194.
Повний текст джерелаАнотація:
The control of cattle tick, Rhipicephalus microplus, is focused on repeated use of acaricides. However, due to growing acaricide resistance and residues problem, immunization of animals along with limited use of effective acaricides is considered a suitable option for the control of tick infestations. To date, more than fifty vaccine candidates have been identified and tested worldwide, but two vaccines were developed using the extensively studied candidate, Bm86. The main reason for limited vaccine commercialization in other countries is genetic diversity in the Bm86 gene leading to considerable variation in vaccine efficacy. India, with 193.46 million cattle population distributed in 28 states and 9 union territories, is suffering from multiple tick infestation dominated by R. microplus. As R. microplus has developed multi-acaricide resistance, an efficacious vaccine may provide a sustainable intervention for tick control. Preliminary experiments revealed that the presently available commercial vaccine based on the BM86 gene is not efficacious against Indian strain. In concert with the principle of reverse vaccinology, genetic polymorphism of the Bm86 gene within Indian isolates of R. microplus was studied. A 578 bp conserved nucleotide sequences of Bm86 from 65 R. microplus isolates collected from 9 Indian states was sequenced and revealed 95.6–99.8% and 93.2–99.5% identity in nucleotides and amino acids sequences, respectively. The identities of nucleotides and deduced amino acids were 94.7–99.8% and 91.8–99.5%, respectively, between full-length sequence (orf) of the Bm86 gene of IVRI-I strain and published sequences of vaccine strains. Six nucleotides deletion were observed in Indian Bm86 sequences. Four B-cell epitopes (D519-K554, H563-Q587, C598-T606, T609-K623), which are present in the conserved region of the IVRI-I Bm86 sequence, were selected. The results confirm that the use of available commercial Bm86 vaccines is not a suitable option against Indian isolates of R. microplus. A country-specific multi-epitope Bm86 vaccine consisting of four specific B-cell epitopes along with candidate molecules, subolesin and tropomyosin in chimeric/co-immunization format may provide a sustainable option for implementation in an integrated tick management system.
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Harry, D. E., D. C. Yang, and J. O. Dawson. "Nucleotide sequence and diversity in 16S ribosomal RNA from Frankia." Plant and Soil 131, no. 1 (February 1991): 143–46. http://dx.doi.org/10.1007/bf00010429.
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Jiang, Qunyi, Shang-Heng Yen, Jiri Stiller, David Edwards, Paul T. Scott, and Peter M. Gresshoff. "Genetic, Biochemical, and Morphological Diversity of the Legume Biofuel Tree Pongamia pinnata." Plant Genetics, Genomics, and Biotechnology 1, no. 3 (June 15, 2017): 54–67. http://dx.doi.org/10.5147/pggb.v1i3.152.
Повний текст джерелаАнотація:
Pongamia pinnata is regarded as a sustainable biofuel feedstock of the future because of its abundant production of oil-rich seeds, tolerance to abiotic stress, and ability to undergo biological nitrogen fixation (minimizing nitrogen inputs). However, it needs extensive domestication through selection and genetic improvement. Owing to its outcrossing nature, Pongamia displays large phenotypic diversity, which is advantageous for selection of desirable phenotypes but problematic for plantation management. In this study, variation was evaluated for seed mass, oil content, and oil composition. To evaluate genetic diversity and to lay the basis for a molecular breeding approach we developed second generation sequencing (2GS)-derived ISSR markers (Pongamia Inter-Simple Sequence Repeats; PISSR). The special feature of PISSRs is that the number of nucleotide repeats and the 5’ and 3’ nucleotide extensions were not arbitrarily chosen, but were based on Pongamia genomic sequences obtained from a NGS (Illumina®) database. Amplification products were resolved by polyacrylamide gel electrophoresis and silver staining or automated capillary electrophoresis to yield distinct and reproducible profiles. Polymorphic bands were excised from polyacrylamide gels and sequenced to reveal similarity to DNA sequences from other legumes. We demonstrated: 1) an abundance of nucleotide core repeats in the Pongamia genome, 2) large genetic and phenotypic diversity among randomly sampled Pongamia trees, 3) restricted diversity in progeny derived from a single mature tree; 4) stability of PISSR markers in Pongamia clones; and 5) genomic DNA sequences within PISSR markers. PISSRs provide a valuable biotechnology tool for assessment of genetic diversity, gene tagging and molecular breeding in Pongamia pinnata.
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Astuti, Dwi, and Siti Nuramaliati Prijono. "Diversity of The Ornate Lorikeet (Trichoglossus ornatus) Birds Based on Mitochondrial DNA Protein Coding Gene." Biosaintifika: Journal of Biology & Biology Education 10, no. 2 (August 29, 2018): 465–71. http://dx.doi.org/10.15294/biosaintifika.v10i2.13501.
Повний текст джерелаАнотація:
Ornate lorikeet (Trichoglossus ornatus) is an endemic bird in Sulawesi. Endemism is one of the factors in declining bird’s population. In the case of the birds conservation programme, information about gene diversity is important for basic strategy. Mitochondrial DNA of animals consists of protein coding genes including ND2 gene. This study informs diversity of the Ornate Lorikeet (Trichoglossus ornatus) birds based on DNA sequences of ND2 gene. DNA total was extracted from blood samples of 21 birds. PCR (Polymerase Chain Reaction) was performed and successfully amplified a single DNA fragment of ND2 gene for all birds. DNA fragments were sequenced and totally 997 base pairs were analyzed. NJ tree was constructed using MEGA5. All DNA sequence data showed that between the birds there were 20 polymorphic (segregating) sites with mean genetic distance was 0.004 ± 0.002 (ranged from 0,000 – 0,008), and had 17 sequence haplotypes (HTor1- HTo17). Haplotype diversity (Hd) was 0.967 ± 0.30387 and nucleotide diversity (Pi) was 0.00439 ± 0.0012. Genetic diversity information could be potential relevance to the breeding management for conservation of the birds.
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Sanchez, P., P. N. Marche, D. Rueff-Juy, and P. A. Cazenave. "Mouse V lambda x gene sequence generates no junctional diversity and is conserved in mammalian species." Journal of Immunology 144, no. 7 (April 1, 1990): 2816–20. http://dx.doi.org/10.4049/jimmunol.144.7.2816.
Повний текст джерелаАнотація:
Abstract The lambda x, a new mouse Ig lambda L chain, is produced by rearrangement of the V lambda x, J lambda 2, and C lambda 2 gene segments. The V lambda x amino acid sequence is as divergent to other V lambda as to Vk gene sequences. Additionally, its third hypervariable region (CDR3) is four amino acids longer than those of all other variable gene segments of murine L chain. We have cloned and sequenced the germ-line V lambda x gene and found that the unexpected CDR3 length is encoded by the V lambda x gene. Junctional diversity is prevented by a TAA termination codon localized at the V lambda x 3' extremity. Moreover, we show a striking conservation of the V lambda x sequence in various mammalian species. Portions of the V lambda x sequence display more than 70% of nucleotide sequence identity with rabbit and human variable regions. These results suggest that V lambda x predated the divergence of mammalian species.
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Crespo, Oscar, Dirk Janssen, Carmen García, and Leticia Ruiz. "Biological and Molecular Diversity of Cucumber green mottle mosaic virus in Spain." Plant Disease 101, no. 6 (June 2017): 977–84. http://dx.doi.org/10.1094/pdis-09-16-1220-re.
Повний текст джерелаАнотація:
The complete RNA genome from Cucumber green mottle mosaic virus (CGMMV) (Alm08), collected during 2009 in cucumber crops located in Spain, was found to be 6,422 nucleotides long. The nucleotide sequence shared the highest identity with isolates from Russia (GQ495274, GQ495275, FJ848666) as do nucleotide sequences of partial CP and MP genes described in Spain since 2005. All the partial genome sequences including RdRp, CP, and MP from 26 isolates collected from 2013 to 2015 in the southeast of Spain, and from seven isolates of other parts of the world, suggest that they grouped in two major clusters: one cluster (I) included 14 isolates collected between 2013 and 2014, and also reference isolates from France, the Netherlands, and Uzbekistan. A second cluster (II) grouped 12 isolates, which were mostly collected in 2015 together with those from Japan, South Korea, and Canada. For the first time, CGMMV isolates of different geographical origin were found coinfecting the same crop and territory. A host range study revealed that representative isolates of cluster II, but not from cluster I, produced local lesions in Chenopodium amaranticolor. RT-PCR using a common primer pair for CGMMV followed by restriction enzyme analysis with KpnI allowed distinguishing cluster I from II CGMMV isolates.
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Vescio, R. A., J. Cao, C. H. Hong, J. C. Lee, C. H. Wu, M. Der Danielian, V. Wu, R. Newman, A. K. Lichtenstein, and J. R. Berenson. "Myeloma Ig heavy chain V region sequences reveal prior antigenic selection and marked somatic mutation but no intraclonal diversity." Journal of Immunology 155, no. 5 (September 1, 1995): 2487–97. http://dx.doi.org/10.4049/jimmunol.155.5.2487.
Повний текст джерелаАнотація:
Abstract The lg VH region sequence in 48 patients with multiple myeloma (MM) was analyzed to characterize the malignant cell of origin. The sequences were obtained after amplification of bone marrow cDNA by using VH family-specific and CH primers, then compared with either directly sequenced patient germ-line or published VH gen sequences to assay for somatic mutation. Because somatic hypermutation of the VH gene occurs late in B cell development, its presence has been helpful in determining the cell of origin in other B cell malignancies. Overall, a median of 8.2% of the nucleotides had evidence of substitution within each VH gene sequence (range=2.7% to 16.5%), which is more prevalent than in any other reported tumor type. Strong evidence of prior antigenic selection pressure was also evident. The ratio of nucleotide substitutions that resulted in amino acid replacement was significantly higher in the complementarity-determining region than in the framework region (3.25 vs 1.56, respectively; p < 0.00005). No VH gene intraclonal diversity was noted, despite sequencing multiple clones (3-16) from each patient, nor was there evidence of further VH gene somatic mutation over the course of three patients' disease. These findings strongly imply that the malignant clone in MM evolves from a cell late in B cell development.
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Wheto, M., O. O. Ismaila, M. A. Adeleke, A. S. Adenaike, S. O. Peters, A. Yakubu, A. O. Adebambo, C. O. N. Ikeobi, and O. A. Adebambo. "Sequence analyses of insulin-like growth factor 1 gene in Nigerian indigenous and arbor acre chickens." Genetika 53, no. 1 (2021): 271–82. http://dx.doi.org/10.2298/gensr2101271w.
Повний текст джерелаАнотація:
Alpha % Indigenous chicken % Gene % Sequence KR nema The chicken Insulin-like growth factor 1 (IGF1) is a candidate gene for growth, body composition and metabolism, skeletal characteristics and growth of adipose tissue and fat deposition in chickens. It is mapped to 165.95 cM on chromosome 1 and composed of four exons and three introns, spanning more than 50 kb. Genomic DNA was extracted from blood samples collected from the experimental birds using Qiagen DNA extraction kits. Polymersae chain reaction (PCR) was carried out using established primers. The PCR amplicon involving 5?untranslated region were sequenced. The sequences were analysed to identify polymorphisms, their genetic diversities and evolutionary relationships among three strains of Nigerian indigenous chickens [Frizzle Feathered (7), Normal Feathered (19) and Naked Neck (19), and the Arbor Acre broiler chicken (17)]. Nucleotide sequences generated were edited and aligned using Codon Code Aligner. Diversity analysis was done using DnaSp while MEGA6 software was used to plot phylogenetic tree using maximum likelihood method. A total of nineteen single nucleotide polymorphisms (SNPs) were detected from 560 bp portions of the 5?UTR among the four chicken populations studied with none detected in the Frizzle feathered chicken. The Naked neck chicken had the highest number of SNP?s (13), haplotypes (6), haplotype diversity (0.778), nucleotide diversity (0.00487), average number of nucleotide differences (2.725), highest number of polymorphic (segregating) sites (13), parsimony informative site (5) and singleton variable site (8). The Naked neck chicken therefore had the highest rate of mutation and degree of allelic variation compared to other chicken strains used in this study. The phylogenetic tree showed that small genetic differentiation exists among the chicken populations studied. Some of the SNPs are newly discovered; hence, association between these alleles and productive traits in Nigerian native chickens is desirable in future studies.
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Jia, Yulin, Gregory T. Bryan, Leonard Farrall, and Barbara Valent. "Natural Variation at the Pi-ta Rice Blast Resistance Locus." Phytopathology® 93, no. 11 (November 2003): 1452–59. http://dx.doi.org/10.1094/phyto.2003.93.11.1452.
Повний текст джерелаАнотація:
The resistance gene Pi-ta protects rice crops against the fungal pathogen Magnaporthe grisea expressing the avirulence gene AVR-Pita in a gene-for-gene manner. Pi-ta, originally introgressed into japonica rice from indica origin, was previously isolated by positional cloning. In this study, we report the nucleotide sequence of a 5,113-base pair region containing a japonica susceptibility pi-ta allele, which has overall 99.6% nucleotide identity to the indica Pi-ta allele conferring resistance. The intron region shows the levels of sequence diversity that typically differentiate genes from indica and japonica rices, but the other gene regions show less diversity. Sequences of the Pi-ta allele from resistant cultivars Katy and Drew from the southern United States are identical to the resistance Pi-ta sequence. Sequences from susceptible cultivars El Paso 144 and Cica 9 from Latin America define a third susceptibility haplotype. This brings the total number of Pi-ta haplotypes identified to four, including the resistance allele and three susceptibility alleles. The Pi-ta locus shows low levels of DNA polymorphism compared with other analyzed R genes. Understanding the natural diversity at the Pi-ta locus is important for designing specific markers for incorporation of this R gene into rice-breeding programs.
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Gatzkaya, S. S., and E. V. Evtushenko. "Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L." Vavilov Journal of Genetics and Breeding 23, no. 2 (March 30, 2019): 135–39. http://dx.doi.org/10.18699/vj19.472.
Повний текст джерелаАнотація:
Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.
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Amimo, Joshua O., Eunice M. Machuka, Edward O. Abworo, Anastasia N. Vlasova, and Roger Pelle. "Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms." Viruses 12, no. 11 (November 5, 2020): 1262. http://dx.doi.org/10.3390/v12111262.
Повний текст джерелаАнотація:
Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.
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Yu, Zhihui, Stephen I. Wright, and Thomas E. Bureau. "Mutator-like Elements in Arabidopsis thaliana: Structure, Diversity and Evolution." Genetics 156, no. 4 (December 1, 2000): 2019–31. http://dx.doi.org/10.1093/genetics/156.4.2019.
Повний текст джерелаАнотація:
Abstract While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu elements in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.
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Oliveira, Hugo, Rita Domingues, Benjamin Evans, J. Mark Sutton, Evelien M. Adriaenssens, and Dann Turner. "Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter." Viruses 14, no. 2 (January 19, 2022): 181. http://dx.doi.org/10.3390/v14020181.
Повний текст джерелаАнотація:
The number of sequenced Acinetobacter phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the Acinetobacter phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting Acinetobacter sp. are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus Obolenskvirus. These results provide an updated view of the viruses infecting Acinetobacter species, providing insights into their diversity.
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Huang, Chi-Ruei, and Szecheng J. Lo. "Evolution and Diversity of the Human Hepatitis D Virus Genome." Advances in Bioinformatics 2010 (February 24, 2010): 1–9. http://dx.doi.org/10.1155/2010/323654.
Повний текст джерелаАнотація:
Human hepatitis delta virus (HDV) is the smallest RNA virus in genome. HDV genome is divided into a viroid-like sequence and a protein-coding sequence which could have originated from different resources and the HDV genome was eventually constituted through RNA recombination. The genome subsequently diversified through accumulation of mutations selected by interactions between the mutated RNA and proteins with host factors to successfully form the infectious virions. Therefore, we propose that the conservation of HDV nucleotide sequence is highly related with its functionality. Genome analysis of known HDV isolates shows that the C-terminal coding sequences of large delta antigen (LDAg) are the highest diversity than other regions of protein-coding sequences but they still retain biological functionality to interact with the heavy chain of clathrin can be selected and maintained. Since viruses interact with many host factors, including escaping the host immune response, how to design a program to predict RNA genome evolution is a great challenging work.
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Oddoye, Sean. "Analysis of The Nucleotide Sequence Diversity of the Lassa Virus and Augmenting its Phylogenetic Tree." STEM Fellowship Journal 4, no. 1 (April 1, 2018): 21–26. http://dx.doi.org/10.17975/sfj-2018-005.
Повний текст джерелаАнотація:
Lassa Virus (LASV) is the etiological catalyst for Lassa fever, an acute hemorrhagic disease with a mortality rate of 15%. Many aspects of the Lassa virus are not understood, like the causation of deafness in ⅓ of surviving patients or why symptoms are benign for 80% of those infected with the virus. Ambiguities like these suggest that there might exist some genomic heterogeneity among infecting viruses and demonstrate a need to quantify and analyze polymorphisms within LASV. Patterns that emerge from phylogenetic trees can be used to assess the structure of a population while also providing insights to the genetic makeup. The purpose of this investigation was to develop a more streamlined means of calculating nucleotide diversity within a subpopulation of Lassa virus strains and to augment a phylogenetic tree of the Lassa Virus glycoprotein precursor (GPC) segment. A total of 25 partial and complete data sequences of LASV strains were obtained from the Genbank Archives. During phase one of this investigation, the sequence data was inputted into MEGA analytical software and the sequence diversity was derived on a nucleotide level. Data from the individual strand sequences was used to augment a phylogenetic tree using Treeview X software. In phase two of this investigation, an algorithm was created using RStudio, with BSGenome and BioStrings extensions. The sequence diversity derived from the statistical analyses on MEGA was compared to that of the algorithm created. A p-value of 0.08 was found, which deviates from the accepted range of non-medical p-value of 0.00 to 0.05. It is suggested that future research focuses on creating a refurbished version of the algorithm to calculate a nucleotide diversity within a percent error of 5%.
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Vidal S., Rodrigo, and Roberto Meléndez C. "Genetic and demographic variation among different colorations of the Eastern South Pacific fish “jerguilla” (Aplodactylus punctatus Valenciennes, 1832) (Perciformes: Aplodactylidae)." Boletín Museo Nacional de Historia Natural 52 (December 26, 2003): 89–95. http://dx.doi.org/10.54830/bmnhn.v52.2003.310.
Повний текст джерелаАнотація:
Colour variation and molecular diversity of Aplodactylus punctatus were addressed with DNA sequence data. Mitochondrial cytochrome b and region control sequences were obtained from representatives of three Chilean populations of this species. Substantial levels of molecular diversity were detected, although there are not relation between the haplotypes obtained and geographical distribution or colour. We consider factors such as geographic distribution, population size, dispersal, secondary contact, and phylopatry as potential causes of the high level of mtDNA nucleotide diversity in this species.
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Liu, F., D. Charlesworth, and M. Kreitman. "The Effect of Mating System Differences on Nucleotide Diversity at the Phosphoglucose Isomerase Locus in the Plant Genus Leavenworthia." Genetics 151, no. 1 (January 1, 1999): 343–57. http://dx.doi.org/10.1093/genetics/151.1.343.
Повний текст джерелаАнотація:
AbstractTo test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.
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Shimatani, Kenichiro. "The Appearance of a Different DNA Sequence May Decrease Nucleotide Diversity." Journal of Molecular Evolution 49, no. 6 (December 1999): 810–13. http://dx.doi.org/10.1007/pl00006604.
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Wang, Yu-Ming, Stuart C. Ray, Oliver Laeyendecker, John R. Ticehurst, and David L. Thomas. "Assessment of Hepatitis C Virus Sequence Complexity by Electrophoretic Mobilities of Both Single-and Double-Stranded DNAs." Journal of Clinical Microbiology 36, no. 10 (1998): 2982–89. http://dx.doi.org/10.1128/jcm.36.10.2982-2989.1998.
Повний текст джерелаАнотація:
To assess genetic variation in hepatitis C virus (HCV) sequences accurately, we optimized a method for identifying distinct viral clones without determining the nucleotide sequence of each clone. Twelve serum samples were obtained from seven individuals soon after they acquired HCV during a prospective study, and a 452-bp fragment from the E2 region was amplified by reverse transcriptase PCR and cloned. Thirty-three cloned cDNAs representing each specimen were assessed by a method that combined heteroduplex analysis (HDA) and a single-stranded conformational polymorphism (SSCP) method to determine the number of clonotypes (electrophoretically indistinguishable cloned cDNAs) as a measure of genetic complexity (this combined method is referred to herein as the HDA+SSCP method). We calculated Shannon entropy, incorporating the number and distribution of clonotypes into a single quantifier of complexity. These measures were evaluated for their correlation with nucleotide sequence diversity. Blinded analysis revealed that the sensitivity (ability to detect variants) and specificity (avoidance of false detection) of the HDA+SSCP method were very high. The genetic distance (mean ± standard deviation) between indistinguishable cloned cDNAs (intraclonotype diversity) was 0.6% ± 0.9%, and 98.7% of cDNAs differed by <2%, while the mean distance between cloned cDNAs with different patterns was 4.0% ± 3.2%. The sensitivity of the HDA+SSCP method compared favorably with either HDA or the SSCP method alone, which resulted in intraclonotype diversities of 1.6% ± 1.8% and 3.5% ± 3.4%, respectively. The number of clonotypes correlated strongly with genetic diversity (R 2, 0.93), but this correlation fell off sharply when fewer clones were assessed. This HDA+SSCP method accurately reflected nucleotide sequence diversity among a large number of viral cDNA clones, which should enhance analyses to determine the effects of viral diversity on HCV-associated disease. If sequence diversity becomes recognized as an important parameter for staging or monitoring of HCV infection, this method should be practical enough for use in laboratories that perform nucleic acid testing.
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Wang, Chih-Li, Arkadiusz Malkus, Sabina M. Zuzga, Pi-Fang Linda Chang, Barry M. Cunfer, Edward Arseniuk, and Peter P. Ueng. "Diversity of the trifunctional histidine biosynthesis gene (his) in cerealPhaeosphaeriaspecies." Genome 50, no. 6 (June 2007): 595–609. http://dx.doi.org/10.1139/g07-038.
Повний текст джерелаАнотація:
Phaeosphaeria species are important causal agents of Stagonospora leaf blotch diseases in cereals. In this study, the nucleotide sequence and deduced polypeptide of the trifunctional histidine biosynthesis gene (his) are used to investigate the phylogenetic relationships and provide molecular identification among cereal Phaeosphaeria species. The full-length sequences of the his gene were obtained by PCR amplification and compared among cereal Phaeosphaeria species. The coding sequence of the his gene in wheat-biotype P. nodorum (PN-w) was 2697 bp. The his genes in barley-biotype P. nodorum (PN-b), two P. avenaria f. sp. triticea isolates (homothallic Pat1 and Pat3), and Phaeosphaeria species from Polish rye and dallis grass were 2694 bp. The his gene in heterothallic isolate Pat2, however, was 2693 bp because the intron had one fewer base. In P. avenaria f. sp. avenaria (Paa), the his gene was only 2670 bp long. The differences in the size of the his gene contributed to the variation in amino acid sequences in the gap region located between the phosphoribosyl-ATP pyrophosphohydrolase and histidinol dehydrogenase sub-domains. Based on nucleotide and deduced amino acid sequences of the his gene, Pat1 was not closely related to either PN-w or the Paa clade. It appears that rates of evolution of the his gene were fast in cereal Phaeosphaeria species. The possible involvement of meiotic recombination in genetic diversity of the his gene in P. nodorum is discussed.
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Hill, Janet E., Robyn P. Seipp, Martin Betts, Lindsay Hawkins, Andrew G. Van Kessel, William L. Crosby, and Sean M. Hemmingsen. "Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing." Applied and Environmental Microbiology 68, no. 6 (June 2002): 3055–66. http://dx.doi.org/10.1128/aem.68.6.3055-3066.2002.
Повний текст джерелаАнотація:
ABSTRACT Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.
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Asri Saffanah Pratiwi and Achmad Taher. "Analisis Polimorfisme Nukleotida Tunggal (SNP) Daerah 3’UTR Gen LDLR Penduduk Papua." Jurnal Natural 15, no. 1 (April 1, 2019): 11–20. http://dx.doi.org/10.30862/jn.v15i1.27.
Повний текст джерелаАнотація:
Single nucleotide polymorphism (SNP) is a single nucleotide difference in the arrangement of DNA base strands that can show genetic variation. The LDLR gene is a low density lipoprotein (LDL-R) receptor gene that functions to regulate cholesterol levels in the blood. The LDLR gene is composed of 18 exons and contains a 3’untranslated region (3’UTR) which plays an important role in regulating gene expression. This study aims to analyze the SNP in an area of 3'UTR LDLR genes from 6 University of Papua students from Papua. The research was carried out by polymerase chain reaction method to multiply the number of target DNA, then sequenced to find out the sequence of nucleotide bases. The results of this study were from 6 individuals, found 2 SNPs at position *52 and *504 with nucleotide diversity (π) of 0.00149. These polymorphisms forms 3 types of haplotypes, namely GG, GA and AA with a haplotype diversity of 0.600 ± 0.215.
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Salerno, Anna, Alexis Delétoile, Martine Lefevre, Ivan Ciznar, Karel Krovacek, Patrick Grimont, and Sylvain Brisse. "Recombining Population Structure of Plesiomonas shigelloides (Enterobacteriaceae) Revealed by Multilocus Sequence Typing." Journal of Bacteriology 189, no. 21 (August 10, 2007): 7808–18. http://dx.doi.org/10.1128/jb.00796-07.
Повний текст джерелаАнотація:
ABSTRACT Plesiomonas shigelloides is an emerging pathogen that is widespread in the aquatic environment and is responsible for intestinal diseases and extraintestinal infections in humans and other animals. Virtually nothing is known about its genetic diversity, population structure, and evolution, which severely limits epidemiological control. We addressed these questions by developing a multilocus sequence typing (MLST) system based on five genes (fusA, leuS, pyrG, recG, and rpoB) and analyzing 77 epidemiologically unrelated strains from several countries and several ecological sources. The phylogenetic position of P. shigelloides within family Enterobacteriaceae was precisely defined by phylogenetic analysis of the same gene portions in other family members. Within P. shigelloides, high levels of nucleotide diversity (average percentage of nucleotide differences between strains, 1.49%) and genotypic diversity (64 distinct sequence types; Simpson's index, 99.7%) were found, with no salient internal phylogenetic structure. We estimated that homologous recombination in housekeeping genes affects P. shigelloides alleles and nucleotides 7 and 77 times more frequently than mutation, respectively. These ratios are similar to those observed in the naturally transformable species Streptococcus pneumoniae with a high rate of recombination. In contrast, recombination within Salmonella enterica, Escherichia coli, and Yersinia enterocolitica was much less frequent. P. shigelloides thus stands out among members of the Enterobacteriaceae. Its high rate of recombination results in a lack of association between genomic background and O and H antigenic factors, as observed for the 51 serotypes found in our sample. Given its robustness and discriminatory power, we recommend MLST as a reference method for population biology studies and epidemiological tracking of P. shigelloides strains.
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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.
Повний текст джерелаАнотація:
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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Gadiou, Sébastien, Otakar Kúdela, Jan Ripl, Frank Rabenstein, Jiban K. Kundu, and Miroslav Glasa. "An Amino Acid Deletion in Wheat streak mosaic virus Capsid Protein Distinguishes a Homogeneous Group of European Isolates and Facilitates Their Specific Detection." Plant Disease 93, no. 11 (November 2009): 1209–13. http://dx.doi.org/10.1094/pdis-93-11-1209.
Повний текст джерелаАнотація:
The tritimovirus Wheat streak mosaic virus (WSMV) is widespread throughout the world and represents a severe threat to cereal crop production. To increase knowledge of genetic diversity of WSMV in Europe, until now scarce, capsid protein (CP) sequences of several Czech, French, Italian, Slovak, and Turkish isolates have been determined. A multiple alignment of CP nucleotide sequences using available WSMV sequences revealed only limited sequence variation among 3 previously sequenced European isolates and the 14 European isolates sequenced in this study. Moreover, these isolates were characterized by an identical 3-nucleotide deletion, resulting in the lack of the Gly2761 codon within the CP region of the polyprotein. The results indicate that this monophyletic group of isolates (designated as WSMV-ΔE) is common and widely dispersed throughout the European continent. The close relationship of WSMV-ΔE isolates implies a single common ancestor and, presumably, subsequent dispersal throughout Europe from a single focus. We developed two simple assays for specific and accurate detection of WSMV-ΔE isolates. First, a conserved ClaI restriction site in the core CP gene sequence unique to WSMV-ΔE isolates was used for restriction fragment length polymorphism analysis of amplified polymerase chain reaction (PCR) products. Second, the conserved and specific codon gap in WSMV-ΔE sequences was used as a target to design specific primers functional in one-step reverse-transcription PCR detection of WSMV-ΔE isolates.
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Clark, Jeremy S. C., Maria Dani, Nigel G. Halford, and Angela Karp. "Evidence of diversity within the SnRK1b gene family of Hordeum species." Genome 48, no. 4 (August 1, 2005): 661–73. http://dx.doi.org/10.1139/g05-024.
Повний текст джерелаАнотація:
Adaptor-specific polymerase chain reaction (PCR) was used to amplify 3 different products, termed variant A, B, and C, from the seed-specific class (SnRK1b) of the sucrose nonfermenting-1-related protein kinase gene family (SnRK1) of different Hordeum species and cultivars of barley (Hordeum vulgare). Standard PCR or reverse transcription-PCR (RT-PCR) at a high temperature, using primers that differed by 1 or 2 nucleotides, was then used to amplify and clone 3 specific variants. One primer pair amplified a variant from I genome species suggesting that this could be a useful I-genome specific marker. The corresponding genes of the 3 variants (A, B, and C) were termed SnRK1b.1, 2, and 3, respectively. SnRK1b.1 and 2, showed 98% – 100% nucleotide sequence identity in the coding region, and 89% – 90% identity in the promoter region (up to 200 bp upstream of the translation start site, ATG). However, they differed in having insertions, deletions, and base pair changes at potentially important sites in the polymerase binding regions. SnRK1b.3 showed 90% nucleotide sequence identity with SnRK1b.1 in the coding region and 86% in the promoter region. This gene predominates in H-genome species within the genus Hordeum and could be a useful marker for this group.Key words: Hordeum, sucrose nonfermenting-1, SNF1-related protein kinase, genetic diversity, metabolic signalling.
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Kilinc, Seyma Gunyakti, Harun Kaya Kesik, and Sami Simsek. "Molecular characterization and haplotypes of sheep and goat isolates of Cysticercus tenuicollis in Turkey." Parasitology 146, no. 8 (May 14, 2019): 1047–54. http://dx.doi.org/10.1017/s0031182019000362.
Повний текст джерелаАнотація:
AbstractTaenia hydatigena, is a common parasite, lived mostly in dogs and wild carnivores in its mature stage, and the larvae, Cysticercus tenuicollis, is found on ruminants and pigs. The aim of the current study was to determine the genetic diversity in 20 isolates of the sheep and goats. After the isolation of total genomic DNA from C. tenuicollis isolates, genetic characterization of the mitochondrial NADH dehydrogenase subunit 1 gene region was amplified using specific JB11–JB12 primers in PCR and the PCR products were sequenced and haplotype and genetic diversity analyses were utilized. As a result, multiple nucleotide changes were determined in the sequence analyses of the isolates leading to detection of 16 and 15 different haplotypes in sheep and goat samples, respectively. These findings are important in terms of showing the diversity of nucleotide variation in C. tenuicollis in Turkey.
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Schaeffer, S. W., and E. L. Miller. "Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region." Genetics 132, no. 2 (October 1, 1992): 471–80. http://dx.doi.org/10.1093/genetics/132.2.471.
Повний текст джерелаАнотація:
Abstract The genetic structure of Drosophila pseudoobscura populations was inferred from a nucleotide sequence analysis of a 3.4-kb segment of the alcohol dehydrogenase (Adh) region. A total of 99 isochromosomal strains collected from 13 populations in North and South America were used to determine if any population departed from a neutral model and to estimate levels of gene flow between populations. This study also included the nucleotide sequences from two sibling species, D. persimilis and D. miranda. We estimated the neutral mutation parameter, 4N mu, in synonymous and noncoding sites for 17 subregions of Adh in each of nine populations with sample sizes greater than three. The nucleotide diversity data in the nine populations was tested for departures from an equilibrium neutral model with two statistical tests. The Tajima and the Hudson, Kreitman, Aguade tests showed that each population fails to reject a neutral model. Tests for genetic differentiation between populations fail to show any population substructure among the North American populations of D. pseudoobscura. The nucleotide diversity data is consistent with direct and indirect measures of gene flow that show extensive dispersal between populations of D. pseudoobscura.