Статті в журналах: "Synteny analysis"

1

Han, F., A. Kleinhofs, S. E. Ullrich, A. Kilian, M. Yano, and T. Sasaki. "Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions." Genome 41, no. 3 (June 1, 1998): 373–80. http://dx.doi.org/10.1139/g98-027.

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The barley (Hordeum vulgare L.) chromosome 1 centromere region contains two adjacent overlapping quantitative trait loci (QTLs) for malting quality traits, and the chromosome 7L subtelomere region contains the stem rust (causal agent Puccinia graminis f.sp. tritici) resistance gene rpg4. To facilitate the saturation mapping of these two target regions, a synteny-based approach was employed. Syntenic relationships between the barley target regions and the rice (Oryza sativa) genome were established through comparative mapping. The barley chromosome 1 centromere region was found to be syntenic with rice chromosome 8 and parts of rice chromosomes 3 and 10. A 6- to 15-fold difference in genetic distance between barley and rice in the syntenic region was observed, owing to the apparent suppressed recombination in the barley chromosome 1 centromere region. Barley chromosome 7L was found to be syntenic with rice chromosome 3. The establishment of synteny with rice in the two target regions allows well-established and characterized rice resources to be utilized in fine mapping and map-based cloning studies.Key words: genome synteny, quantitative trait loci, QTL, disease resistance gene, Triticeae.

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2

Pandey, Manmohan, Basdeo Kushwaha, Ravindra Kumar, Prachi Srivastava, Suman Saroj, and Mahender Singh. "Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes." Journal of Heredity 111, no. 5 (July 2020): 486–90. http://dx.doi.org/10.1093/jhered/esaa025.

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Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

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3

Lee, Jongin, Woon-young Hong, Minah Cho, Mikang Sim, Daehwan Lee, Younhee Ko, and Jaebum Kim. "Synteny Portal: a web-based application portal for synteny block analysis." Nucleic Acids Research 44, W1 (May 6, 2016): W35—W40. http://dx.doi.org/10.1093/nar/gkw310.

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4

Morán Losada, Patricia, and Burkhard Tümmler. "SNP synteny analysis ofStaphylococcus aureusandPseudomonas aeruginosapopulation genomics." FEMS Microbiology Letters 363, no. 19 (October 2016): fnw229. http://dx.doi.org/10.1093/femsle/fnw229.

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5

Zhao, Tao, and M. Eric Schranz. "Network approaches for plant phylogenomic synteny analysis." Current Opinion in Plant Biology 36 (April 2017): 129–34. http://dx.doi.org/10.1016/j.pbi.2017.03.001.

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6

Pan, X., L. Stein, and V. Brendel. "SynBrowse: a synteny browser for comparative sequence analysis." Bioinformatics 21, no. 17 (June 30, 2005): 3461–68. http://dx.doi.org/10.1093/bioinformatics/bti555.

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7

Xu, Yiqing, Changwei Bi, Guoxin Wu, Suyun Wei, Xiaogang Dai, Tongming Yin, and Ning Ye. "VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/7823429.

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Background. In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output. Implementation. To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF). Result. Users can upload sequence alignments from blast and collinearity relationship from the synteny analysis tools. The website can generate the vector or raster graphical results automatically. We also provide a java-based bytecode binary to enable the command-line execution.

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8

Stirling, Brigid, Zamin Koo Yang, Lee E. Gunter, Gerald A. Tuskan, and H. D. Bradshaw Jr. "Comparative sequence analysis between orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity." Canadian Journal of Forest Research 33, no. 11 (November 1, 2003): 2245–51. http://dx.doi.org/10.1139/x03-155.

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More than 300 kb of DNA sequence from five Populus bacterial artificial chromosome (BAC) clones was compared with the complete sequence of the Arabidopsis genome to search for collinearity between the genomes of these two plant genera. Approximately 27% of the DNA sequences from the Populus genome were homologous to protein-coding regions in the Arabidopsis genome. BLAST scores and synteny were used to infer orthologous relationships between the Populus and Arabidopsis homologs. The probability that any pair of genes on a single Populus BAC will have orthologs on the same Arabidopsis chromosome is 46%58%, substantially greater than the 20% expectation if there is no conservation of synteny between the Populus and Arabidopsis genomes. Likewise, the probability that any pair of genes on a single Populus BAC will have orthologs on a single Arabidopsis BAC is 19%25%, much higher than the 0.1% expected if the orthologs are randomly distributed. These results provide evidence for substantial "pockets" of conserved microcollinearity between regions of the Populus and Arabidopsis genomes as well as for conservation of synteny even when local gene collinearity is not preserved during genome evolution.

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9

Kato, K., H. Miura, and S. Sawada. "Comparative mapping of the wheat Vrn-AI region with the rice Hd-6 region." Genome 42, no. 2 (April 1, 1999): 204–9. http://dx.doi.org/10.1139/g98-115.

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Although extensive synteny between hexaploid wheat and rice chromosomes has been demonstrated, synteny between the species breaks down in several regions of the wheat genome carrying agronomically important genes. A possible relationship between the wheat Vrn-A1, the vernalization response gene on chromosome 5A, and the rice Hd-6, a QTL controlling heading date by photoperiod response on chromosome 3, was investigated. Rice cDNA clones which had previously been mapped onto the Hd-6 region were screened for comparative genetic mapping of the Vrn-A1 region. Ten markers mapped to Hd-6 were assigned to wheat chromosome 5A by nullisomic-tetrasomic analysis. Of them, four cDNA markers, linked within 2.2 cM in the rice Hd-6 region, were mapped on the flanking region of the wheat Vrn-A1, with a complete correspondence of order, demonstrating a fine-scale genetic collinearity. These results gave evidence that the wheat Vrn-A1 region is in synteny with the rice Hd-6 region.Key words: wheat, rice, vernalization response gene, photoperiod response gene, synteny.

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10

Matsunaga, Sachihiro, and Akihiro Nakaya. "Computational Synteny Analysis Promotes a Better Understanding of Chromosome Evolution." CYTOLOGIA 82, no. 2 (2017): 101–4. http://dx.doi.org/10.1508/cytologia.82.101.

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11

Zhou, Qiuzhong, Yuxi Jiang, Chaoqun Cai, Wen Li, Melvin Khee-Shing Leow, Yi Yang, Jin Liu, Dan Xu, and Lei Sun. "Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs." Life Science Alliance 6, no. 6 (April 5, 2023): e202302002. http://dx.doi.org/10.26508/lsa.202302002.

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Although long noncoding RNAs (lncRNAs) experience weaker evolutionary constraints and exhibit lower sequence conservation than coding genes, they can still conserve their features in various aspects. Here, we used multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1,731 conserved lncRNAs with 427 high-confidence ones meeting multiple criteria. Conserved lncRNAs, compared with non-conserved ones, generally have longer gene bodies, more exons and transcripts, stronger connections with human diseases, and are more abundant and widespread across different tissues. Transcription factor (TF) profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger regulation on conserved than non-conserved lncRNAs. Our study has reconciled some discrepant interpretations of lncRNA conservation and revealed a new set of transcriptional factors ruling the expression of conserved lncRNAs.

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12

Cho, Yeonghun, Insu Lim, and Jungmin Ha. "Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species." Agronomy 13, no. 8 (August 10, 2023): 2100. http://dx.doi.org/10.3390/agronomy13082100.

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Rice is a vital staple food crop worldwide, providing nutrition and sustenance to a significant portion of the global population. The genetic diversity of cultivated rice species has been significantly reduced during domestication, resulting in the loss of favorable alleles. To overcome this limitation, wild rice species have been used in introgression breeding programs to introduce beneficial alleles. In this study, we performed syntenic and phylogenetic analyses for 10 Oryza species, comprising both cultivar and wild species. Pairwise syntenic analysis revealed 3885 synteny blocks containing 1,023,342 gene pairs among 10 species. O. nivara contained the most blocks that were syntenous with the other nine species. In total, 425 paralogous and orthologous genes were identified for 30 key genes involved in rice breeding. His1 (43), GS3 (28), and qSW5/GW5 (27) had the most paralogous and orthologous genes. For GS3 and qSW5/GW5, two gene transfer events were detected. These findings have implications for rice breeding strategies, particularly with respect to gene pyramiding and introgression breeding programs. This research will contribute to the development of elite cultivars with improved quality and yield to meet the growing global demand for high-quality rice.

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13

Zhao, Tao, and M. Eric Schranz. "Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes." Proceedings of the National Academy of Sciences 116, no. 6 (January 23, 2019): 2165–74. http://dx.doi.org/10.1073/pnas.1801757116.

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A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.

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14

Ehrlich, Jason, David Sankoff, and Joseph H. Nadeau. "Synteny Conservation and Chromosome Rearrangements During Mammalian Evolution." Genetics 147, no. 1 (September 1, 1997): 289–96. http://dx.doi.org/10.1093/genetics/147.1.289.

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Abstract An important problem in comparative genome analysis has been defining reliable measures of synteny conservation. The published analytical measures of synteny conservation have limitations. Nonindependence of comparisons, conserved and disrupted syntenies that are as yet unidentified, and redundant rearrangements lead to systematic errors that tend to overestimate the degree of conservation. We recently derived methods to estimate the total number of conserved syntenies within the genome, counting both those that have already been described and those that remain to be discovered. With this method, we show that ~65% of the conserved syntenies have already been identified for humans and mice, that rates of synteny disruption vary ~25-fold among mammalian lineages, and that despite strong selection against reciprocal translocations, inter-chromosome rearrangements occurred approximately fourfold more often than inversions and other intra-chromosome rearrangements, at least for lineages leading to humans and mice.

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15

Tsubokura, Yasutaka, Ryutaku Onda, Shusei Sato, Zhengjun Xia, Masaki Hayashi, Yukie Fukushima, Satoshi Tabata, and Kyuya Harada. "Characterization of soybean genome based on synteny analysis with Lotus japonicus." Breeding Science 58, no. 2 (2008): 157–67. http://dx.doi.org/10.1270/jsbbs.58.157.

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16

Dupré, Délia, and Hervé Tostivint. "Evolution of the gastrin–cholecystokinin gene family revealed by synteny analysis." General and Comparative Endocrinology 195 (January 2014): 164–73. http://dx.doi.org/10.1016/j.ygcen.2013.10.019.

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17

Guo, Li, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin Ning, Zhesi He, Roxana Teodor, et al. "The opium poppy genome and morphinan production." Science 362, no. 6412 (August 30, 2018): 343–47. http://dx.doi.org/10.1126/science.aat4096.

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Morphinan-based painkillers are derived from opium poppy (Papaver somniferumL.). We report a draft of the opium poppy genome, with 2.72 gigabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 1.77 and 204 megabases, respectively. Synteny analysis suggests a whole-genome duplication at ~7.8 million years ago and ancient segmental or whole-genome duplication(s) that occurred before the Papaveraceae-Ranunculaceae divergence 110 million years ago. Syntenic blocks representative of phthalideisoquinoline and morphinan components of a benzylisoquinoline alkaloid cluster of 15 genes provide insight into how this cluster evolved. Paralog analysis identified P450 and oxidoreductase genes that combined to form theSTORRgene fusion essential for morphinan biosynthesis in opium poppy. Thus, gene duplication, rearrangement, and fusion events have led to evolution of specialized metabolic products in opium poppy.

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18

Ota, Yuko, and Martin Flajnik. "Comparative analysis of Xenopus immune-related genes (43.22)." Journal of Immunology 184, no. 1_Supplement (April 1, 2010): 43.22. http://dx.doi.org/10.4049/jimmunol.184.supp.43.22.

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Abstract Evolutionarily, Xenopus species shared a common ancestor with humans ~350 million years ago, and it is one of the high connectivity animals linking mammals to lower vertebrate taxa. Through an in silico approach, we have uncovered many new genes that have important roles in the Xenopus immune system and have analyzed their syntenic relationships relative to other vertebrates. We found that, in contrast to teleost fish, the genomic synteny is remarkably similar between the human and Xenopus, yet in some cases apparent ancestral syntenies can be still found only in the Xenopus genome. We predict that the evolutionarily conserved genes might have vital roles in fundamental immune function, whereas novel genes found only in particular species, especially those within ancient linkage groups, could impart new insights into the immune system. We are specifically interested in the genes that belong to the variable (V) and the constant (C1)-type of the immunoglobulin superfamily (IgSF), including immunoglobulin, T cell receptor, MHC, and B7. In order to understand the phylogenetic relationship and the evolutionary history of these gene families, we used comparative approach; database searches and comparative genomics among different vertebrate classes. Our analysis revealed insights into the architecture of the primordial immune complex that might have played important roles during evolution.

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Iqbal, Muhammad Munir, William Erskine, Jens D. Berger, and Matthew N. Nelson. "Phenotypic characterisation and linkage mapping of domestication syndrome traits in yellow lupin (Lupinus luteus L.)." Theoretical and Applied Genetics 133, no. 10 (July 18, 2020): 2975–87. http://dx.doi.org/10.1007/s00122-020-03650-9.

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AbstractThe transformation of wild plants into domesticated crops usually modifies a common set of characters referred to as ‘domestication syndrome’ traits such as the loss of pod shattering/seed dehiscence, loss of seed dormancy, reduced anti-nutritional compounds and changes in growth habit, phenology, flower and seed colour. Understanding the genetic control of domestication syndrome traits facilitates the efficient transfer of useful traits from wild progenitors into crops through crossing and selection. Domesticated forms of yellow lupin (Lupinus luteus L.) possess many domestication syndrome traits, while their genetic control remains a mystery. This study aimed to reveal the genetic control of yellow lupin domestication traits. This involved phenotypic characterisation of those traits, defining the genomic regions controlling domestication traits on a linkage map and performing a comparative genomic analysis of yellow lupin with its better-understood relatives, narrow-leafed lupin (L. angustifolius L.) and white lupin (L. albus L.). We phenotyped an F9 recombinant inbred line (RIL) population of a wide cross between Wodjil (domesticated) × P28213 (wild). Vernalisation responsiveness, alkaloid content, flower and seed colour in yellow lupin were each found to be controlled by single loci on linkage groups YL-21, YL-06, YL-03 and YL-38, respectively. Aligning the genomes of yellow with narrow-leafed lupin and white lupin revealed well-conserved synteny between these sister species (76% and 71%, respectively). This genomic comparison revealed that one of the key domestication traits, vernalisation-responsive flowering, mapped to a region of conserved synteny with the vernalisation-responsive flowering time Ku locus of narrow-leafed lupin, which has previously been shown to be controlled by an FT homologue. In contrast, the loci controlling alkaloid content were each found at non-syntenic regions among the three species. This provides a first glimpse into the molecular control of flowering time in yellow lupin and demonstrates both the power and the limitation of synteny as a tool for gene discovery in lupins.

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20

De Quadros, Luiz Henrique Bovi, Luís Gustavo Gomos Lobo, Edinara Maria Barbosa, Heris Lorenzi Dos Santos, Dayane Lorenzi Dos Santos, Silvia Graciele Hülse De Souza, and Tiago Benedito Dos Santos. "In silico analysis of superoxide dismutase family genes in Ipomoea trifida L." DELOS: DESARROLLO LOCAL SOSTENIBLE 16, no. 48 (October 29, 2023): 3223–39. http://dx.doi.org/10.55905/rdelosv16.n48-017.

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Superoxide dismutase (SOD) is described as a key enzyme in the antioxidant system of plants. It plays a vital role in protecting plants against various biotic and abiotic stresses by scavenging reactive oxygen species (ROS) produced by organisms. The SODs genes family has been documented in several plant species, but its characterization in Ipomoea trifida has not been reported. In the present study, the family of SODs genes present in the genome of I. trifida was comprehensively analyzed. Analysis can be performed using bioinformatics tools, physicochemical characterization of proteins, gene structure analysis (exon/intron), phylogenetic relationships, synteny, and expression profile analysis. We identified seven SODs genes, including four Cu/Zn-SOD (CSD), two Fe-SOD (FSD), and one Mn-SOD (MSD), and based on phylogenetic analysis, the SODs genes were classified and divided into three main groups based on their metal cofactor. Synteny analysis revealed eight pairs among SOD genes sweet potato and Arabidopsis. The in silico expression profile showed that ItfSODs genes were differentially expressed. The results of this study provide relevant information for further research of ItfSODs genes in I. trifida aiming to promote the molecular improvement of sweet potato.

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21

Hausken, Krist, and Berta Levavi-Sivan. "Synteny and phylogenetic analysis of paralogous thyrostimulin beta subunits (GpB5) in vertebrates." PLOS ONE 14, no. 9 (September 19, 2019): e0222808. http://dx.doi.org/10.1371/journal.pone.0222808.

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Xu, Pei, Tingting Hu, Yuejian Yang, Xiaohua Wu, Baogen Wang, Yonghua Liu, Dehui Qin, et al. "Mapping Genes Governing Flower and Seedcoat Color in Asparagus Bean (Vigna unguiculata ssp. sesquipedalis) Based on Single Nucleotide Polymorphism and Simple Sequence Repeat Markers." HortScience 46, no. 8 (August 2011): 1102–4. http://dx.doi.org/10.21273/hortsci.46.8.1102.

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Colors of flower and seedcoat are interesting traits of asparagus bean, a cultivated subspecies of cowpea grown throughout Asia for its tender, long green pods. Little is known about the inheritance of these traits including their genome location. We report here the genetic analysis and mapping of the genes governing flower and seedcoat color in asparagus bean based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. Analysis of the F1 and F7:8 generation of recombinant inbred lines (RILs) population showed a monogenetic inheritance of both traits. Purple flower and brown seedcoat are dominant over white flower and cream seedcoat, respectively. We further show that genes governing flower color and seedcoat color are tightly linked on LG8, ≈0.4 cM apart. Synteny analysis showed that the gene controlling seedcoat color in our study is syntenic to the soybean T locus. The use of the mapping information in asparagus bean breeding is discussed.

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23

OMRAN, HEYMUT, KARSTEN HÄFFNER, SUSE BURTH, CARMEN FERNANDEZ, BERNARDO FARGIER, AMINTA VILLAQUIRAN, HANS-GERD NOTHWANG, et al. "Human Adolescent Nephronophthisis: Gene Locus Synteny with Polycystic Kidney Disease in Pcy Mice." Journal of the American Society of Nephrology 12, no. 1 (January 2001): 107–13. http://dx.doi.org/10.1681/asn.v121107.

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Abstract. In a large Venezuelan kindred, a new type of nephronophthisis was recently identified: Adolescent nephronophthisis (NPH3) is a late-onset recessive renal cystic disorder of the nephronophthisis/medullary cystic group of diseases causing end-stage renal disease at a median age of 19 yr. With the use of a homozygosity mapping strategy, the gene (NPHP3) was previously localized to chromosome 3q22 within a critical interval of 2.4 cM. In the current study, the NPHP3 genetic region was cloned and seven genes, eight expressed sequence-tagged sites, and seven microsatellites were physically localized within the critical disease interval. By human-mouse synteny analysis based on expressed genes, synteny between the human NPHP3 locus on chromosome 3q and the pcy locus on mouse chromosome 9 was clearly demonstrated, thus providing the first evidence of synteny between a human and a spontaneous murine renal cystic disease. By fluorescence in situ hybridization the chromosomal assignment of NPHP3 to chromosome 3q21-q22 was refined. Renal pathology in NPH3 was found to consist of tubular basement membranes changes, tubular atrophy and dilation, and sclerosing tubulointerstitial nephropathy. This pathology clearly resembled findings observed in the recessive pcy mouse model of late-onset polycystic kidney disease. In analogy to pcy, renal cyst development at the corticomedullary junction was found to be an early sign of the disease. Through cloning of the NPH3 critical region and mapping of expressed genes, synteny between human NPH3 and murine pcy was established, thus generating the hypothesis that both diseases are caused by recessive mutations of homologous genes.

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24

McLysaght, Aoife, Anton J. Enright, Lucy Skrabanek, and Kenneth H. Wolfe. "Estimation of Synteny Conservation and Genome Compaction Between Pufferfish (Fugu) and Human." Yeast 1, no. 1 (2000): 22–36. http://dx.doi.org/10.1002/(sici)1097-0061(200004)17:1<22::aid-yea5>3.0.co;2-s.

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Background: Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrateFugu rubripes(pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human andFuguwere studied using data from public databases.Methods: Intron length and map positions of human andFuguorthologues were compared to analyse relative genome compaction and synteny conservation respectivley. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data.Results: Analysis of 199 introns in 22 orthologous genes showed an eight-fold average size reduction inFugu, consistent with the ratio of total genome sizes. There was no consistent pattern relating the size reduction in individual introns or genes to gene base composition in either species. For genes that are neighbours inFugu(genes from the same cosmid or GenBank entry), 40–50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incomplete human genome sequence data and the existence of dispersed gene families. Some genes that are neighbours inFuguhave human orthologues that are several megabases and tens of genes apart. This is probably caused by small inversions or other intrachromosomal rearrangements.Conclusions: Comparison of observed data to computer simulations suggests that 4000–16 000 chromosomal rearrangements have occured sinceFuguand human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons.

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25

Ciurko, Dominika, Cécile Neuvéglise, Maciej Szwechłowicz, Zbigniew Lazar, and Tomasz Janek. "Comparative Analysis of the Alkaline Proteolytic Enzymes of Yarrowia Clade Species and Their Putative Applications." International Journal of Molecular Sciences 24, no. 7 (March 30, 2023): 6514. http://dx.doi.org/10.3390/ijms24076514.

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Proteolytic enzymes are commercially valuable and have multiple applications in various industrial sectors. The most studied proteolytic enzymes produced by Yarrowia lipolytica, extracellular alkaline protease (Aep) and extracellular acid protease (Axp), were shown to be good candidates for different biotechnological applications. In this study, we performed a comprehensive analysis of the alkaline proteolytic enzymes of Yarrowia clade species, including phylogenetic studies, synteny analysis, and protease production and application. Using a combination of comparative genomics approaches based on sequence similarity, synteny conservation, and phylogeny, we reconstructed the evolutionary scenario of the XPR2 gene for species of the Yarrowia clade. Furthermore, except for the proteolytic activity of the analyzed Yarrowia clade strains, the brewers’ spent grain (BSG) was used as a substrate to obtain protein hydrolysates with antioxidant activity. For each culture, the degree of hydrolysis was calculated. The most efficient protein hydrolysis was observed in the cultures of Y. lipolytica, Y. galli, and Y. alimentaria. In contrast, the best results obtained using the 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) method were observed for the culture medium after the growth of Y. divulgata, Y. galli, and Y. lipolytica on BSG.

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d'Aloisio, E., A. R. Paolacci, A. P. Dhanapal, O. A. Tanzarella, E. Porceddu, and M. Ciaffi. "Protein disulphide isomerase family in bread wheat (Triticum aestivum L.): genomic structure, synteny conservation and phylogenetic analysis." Plant Genetic Resources 9, no. 2 (May 4, 2011): 342–46. http://dx.doi.org/10.1017/s1479262111000232.

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Eight genes encoding protein disulphide isomerase (PDI)-like proteins in bread wheat were cloned and characterized and their genomic structure was compared with that of homoeologous genes isolated from other plant species. Fourteen wheat cDNA sequences of PDI-like genes were amplified and cloned; eight of them were relative to distinct PDI-like genes, whereas six corresponded to homoeologous sequences. Also, the genomic sequences of the eight non-homoeologous genes were amplified and cloned. Phylogenetic analysis, which included eight genes encoding PDI-like proteins and the gene encoding the typical PDI, assigned at least one of them to each of the eight major clades identified in the phylogenetic tree of the PDI gene family of plants. The close chromosome synteny between wheat and rice was confirmed by the location of the homoeologous genes of the PDI family in syntenic regions of the two species. Within the same phylogenetic group, a high level of conservation, in terms of sequence homology, genomic structure and domain organization, was detected between wheat and the other plant species. The high level of conservation of sequence and genomic organization within the PDI gene family, even between distant plant species, might be ascribed to the key metabolic roles of their protein products.

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Bayır, Mehtap, and Gökhan Arslan. "Balon Balığı (Fugu rubripes)’nda Katalaz Geninin Biyoinformatik Analizleri." Turkish Journal of Agriculture - Food Science and Technology 8, no. 6 (June 26, 2020): 1413–17. http://dx.doi.org/10.24925/turjaf.v8i6.1413-1417.3353.

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In this study, bioinformatics analysis of fugu (Fugu rubripes) catalase (cat) gene was performed. Molecular biology science is developing rapidly in parallel with the increasing importance of bioinformatics, thanks to the developed techniques in recent years. In this bioinformatics-based study wich enables the effective identification and characterization of genes in living organisms using online genome databases and statistics and storage, organization and sharing of the ever-increasing genetic data we designed the conserved gene synteny and gene structure and detected the identiy-similarity ratios between fugu and the other telosts and tetrapods. NCBI-GeneBank, EMBL, ENSEML and UNIPROT databases have been used for all these bioinformatics studies. Bioedit and Mega programs were used to perform the analysis and evaluate the data obtained from all these databases. In silico analysis such as the identification and characterization of fugu cat gene, exons-introns organization, phylogenetic tree and gene synteny were completed in this study and presented with tables and figures.

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Hirai, Hirohisa, Yasuhiro Go, Yuriko Hirai, Gilbert Rakotoarisoa, Joko Pamungkas, Sudarath Baicharoen, Israt Jahan, Dondin Sajuthi, and Anthony J. Tosi. "Considerable Synteny and Sequence Similarity of Primate Chromosomal Region VIIq31." Cytogenetic and Genome Research 158, no. 2 (2019): 88–97. http://dx.doi.org/10.1159/000500796.

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Human chromosome 7 has been the focus of many behavioral, genetic, and medical studies because it carries genes related to cancer and neurodevelopment. We examined the evolution of the chromosome 7 homologs, and the 7q31 region in particular, using chromosome painting analyses and 3 paint probes derived from (i) the whole of chimpanzee chromosome VII (wcVII), (ii) human 7q31 (h7q31), and (iii) the chimpanzee homolog VIIq31 (cVIIq31). The wcVII probe was used instead of the whole human chromosome 7 because the chimpanzee contains additional C-bands and revealed large areas of synteny conservation as well as fragmentation across 20 primate species. Analyses focusing specifically on the 7q31 homolog and vicinity revealed considerable conservation across lineages with 2 exceptions. First, the probes verified an insertion of repetitive sequence at VIIq22 in chimpanzees and bonobos and also detected the sequence in most subtelomeres of the African apes. Second, a paracentric inversion with a breakpoint in the cVIIq31 block was found in the common marmoset, confirming earlier studies. Subsequent in silico comparative genome analysis of 17 primate species revealed that VIIq31.1 is more significantly conserved at the sequence level than other regions of chromosome VII, which indicates that its components are likely responsible for critical shared traits across the order, including conditions necessary for proper human development and wellbeing.

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McLysaght, Aoife, Anton J. Enright, Lucy Skrabanek, and Kenneth H. Wolfe. "Estimation of Synteny Conservation and Genome Compaction Between Pufferfish (Fugu) and Human." Yeast 1, no. 1 (January 1, 2000): 22–36. http://dx.doi.org/10.1155/2000/234298.

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Background: Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrate Fugu rubripes (pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human and Fugu were studied using data from public databases.Methods: Intron length and map positions of human and Fugu orthologues were compared to analyse relative genome compaction and synteny conservation respectivley. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data.Results: Analysis of 199 introns in 22 orthologous genes showed an eight-fold average size reduction in Fugu, consistent with the ratio of total genome sizes. There was no consistent pattern relating the size reduction in individual introns or genes to gene base composition in either species. For genes that are neighbours in Fugu (genes from the same cosmid or GenBank entry), 40–50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incomplete human genome sequence data and the existence of dispersed gene families. Some genes that are neighbours in Fugu have human orthologues that are several megabases and tens of genes apart. This is probably caused by small inversions or other intrachromosomal rearrangements.Conclusions: Comparison of observed data to computer simulations suggests that 4000–16 000 chromosomal rearrangements have occured since Fugu and human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons.

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30

Jiang, Rays H. Y., Brett M. Tyler, and Francine Govers. "Comparative Analysis of Phytophthora Genes Encoding Secreted Proteins Reveals Conserved Synteny and Lineage-Specific Gene Duplications and Deletions." Molecular Plant-Microbe Interactions® 19, no. 12 (December 2006): 1311–21. http://dx.doi.org/10.1094/mpmi-19-1311.

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Comparative analysis of two Phytophthora genomes revealed overall colinearity in four genomic regions consisting of a 1.5-Mb sequence of Phytophthora sojae and a 0.9-Mb sequence of P. ramorum. In these regions with conserved synteny, the gene order is largely similar; however, genome rearrangements also have occurred. Deletions and duplications often were found in association with genes encoding secreted proteins, including effectors that are important for interaction with host plants. Among secreted protein genes, different evolutionary patterns were found. Elicitin genes that code for a complex family of highly conserved Phytophthora-specific elicitors show conservation in gene number and order, and often are clustered. In contrast, the race-specific elicitor gene Avr1b-1 appeared to be missing from the region with conserved synteny, as were its five homologs that are scattered over the four genomic regions. Some gene families encoding secreted proteins were found to be expanded in one species compared with the other. This could be the result of either repeated gene duplications in one species or specific deletions in the other. These different evolutionary patterns may shed light on the functions of these secreted proteins in the biology and pathology of the two Phytophthora spp.

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Wang, Y., H. Tang, J. D. DeBarry, X. Tan, J. Li, X. Wang, T. h. Lee, et al. "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity." Nucleic Acids Research 40, no. 7 (January 4, 2012): e49-e49. http://dx.doi.org/10.1093/nar/gkr1293.

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Tello, J. A., S. Wu, J. E. Rivier, and N. M. Sherwood. "Four functional GnRH receptors in zebrafish: analysis of structure, signaling, synteny and phylogeny." Integrative and Comparative Biology 48, no. 5 (April 19, 2008): 570–87. http://dx.doi.org/10.1093/icb/icn070.

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Marquioni, Vinicius, Luiz Antonio Carlos Bertollo, Débora Diniz, and Marcelo de Bello Cioffi. "Comparative chromosomal mapping in Triportheus fish species. Analysis of synteny between ribosomal genes." Micron 45 (February 2013): 129–35. http://dx.doi.org/10.1016/j.micron.2012.11.008.

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34

Dong, Zhi-Gang, Hui Liu, Xiao-Long Wang, Jun Tang, Kai-Kai Zhu, Yong-Hui Wu, Xin-Lu Chen, Xiao-Ping Tang, and Zong-Ming (Max) Cheng. "Evolution of Acyl-CoA-binding protein gene family in plants provides insights into potential functions of grapevine (Vitis vinifera L.)." Journal of Berry Research 10, no. 4 (December 15, 2020): 677–96. http://dx.doi.org/10.3233/jbr-200528.

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BACKGROUND: Grapevine was one of the most important perennial fruit crops worldwide. Acyl-CoA-binding proteins (ACBPs) in eudicots and monocots show conservation in an acyl-CoA-binding domain (ACB domain) which binds acyl-CoA esters. OBJECTIVE: The information and data provided in the present study contributes to understand the evolutionary processes and potential functions of this gene family in grapevine growth and development, and responses to abiotic stress. METHODS: Using the complete grapevine genome sequences, we investigated the number grapevine ACBP genes, the exon-intron structure, phylogenetic relationships and synteny with the Arabidopsis ACBP gene family. Furthermore, the expression profiles of VvACBP genes based on public microarray data in different tissues, and the expression patterns responding to different exogenous hormones as well as abiotic and biotic stresses were presented. The qRT-PCR was used to verify the microarray data under drought stress treatments. Finally, the leaf relative water content (RWC), leaf chlorophyll content, and enzymatic activities were measured to further examine the tolerance to drought stress in grapevine. RESULTS: The six grapevine ACBPs were identified. Their distribution into various groups differed from Arabidopsis and rice. Synteny analysis demonstrated that several VvACBP genes were found in corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of the respective lineages. Sequence alignment and structural annotation provided an overview of variations that might contribute to functional divergence from Arabidopsis ACBPs. Expressional analyses suggested that both conserved and variant biological functions exist in ACBPs across different species. The expression pattern of these genes were similar in the microarray and qRT-PCR analyses. Gene structure organization and expression characteristics of VvACBPs resembled those of their Arabidopsis orthologous, although species-specific differences also exist. Differential regulation of genes suggested functional diversification among isoforms. The biochemical and physiological data showed the tolerance to drought stress of grapevine. CONCLUSIONS: These findings provided insight into evolution of ACBP gene family in plants and a solid foundation for a deeper understanding of the complex molecular responses of grapevine to stress.

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Zhu, Liming, Hao Fang, Ziming Lian, Jingbo Zhang, Xinle Li, Jisen Shi, Lu Lu, Ye Lu, Jinhui Chen, and Tielong Cheng. "Genome-Wide Investigation and Expression Analysis of the Nitraria sibirica Pall. CIPK Gene Family." International Journal of Molecular Sciences 23, no. 19 (September 30, 2022): 11599. http://dx.doi.org/10.3390/ijms231911599.

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The calcineurin B-like-interacting protein kinase (CIPK) protein family plays a key role in the plant calcium ion-mediated signal transduction pathway, which regulates a plant’s response to abiotic stress. Nitraria sibirica pall. (N. sibirica) is a halophyte with a strong tolerance for high salt environments, yet how it is able to deal with salt stress on a molecular level is still unknown. Due to their function as described in other plant species, CIPK genes are prime candidates for a role in salt stress signaling in N. sibirica. In this study, we identified and analyzed the phylogenetic makeup and gene expression of the N. sibirica CIPK gene family. A total of 14 CIPKs were identified from the N. sibirica genome and were clustered into seven groups based on their phylogeny. The promoters of NsCIPK genes contained multiple elements involved in hormonal and stress response. Synteny analysis identified a total of three pairs of synteny relationships between NsCIPK genes. Each gene showed its own specific expression pattern across different tissues, with the overall expression of CIPK6 being the lowest, and that of CIPK20 being the highest. Almost all CIPK genes tended to respond to salt, drought, and cold stress, but with different sensitivity levels. In this study, we have provided a general description of the NsCIPK gene family and its expression, which will be of great significance for further understanding of the NsCIPK gene family function.

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Zhou, Yong, Yuan Cheng, Chunpeng Wan, Jingwen Li, Youxin Yang, and Jinyin Chen. "Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon." PeerJ 8 (February 17, 2020): e8358. http://dx.doi.org/10.7717/peerj.8358.

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The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

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Raghuvanshi, Saurabh, Subodh K. Srivastava, Anupama Gaur, Ajit K. Pal, Vivek Dalal, Archana Singh, Irfan A. Ghazi, et al. "Sequence analysis of the long arm of rice chromosome 11 for rice?wheat synteny." Functional & Integrative Genomics 4, no. 2 (May 1, 2004): 102–17. http://dx.doi.org/10.1007/s10142-004-0109-y.

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Zhang, Yanjie, Yu Ma, Ruiqi Liu, and Guanglin Li. "Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana." International Journal of Molecular Sciences 23, no. 1 (January 3, 2022): 511. http://dx.doi.org/10.3390/ijms23010511.

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K-homologous (KH) family is a type of nucleic acid-binding protein containing the KH domain and has been found to affect splicing and transcriptional regulation. However, KH family genes haven’t been investigated in plant species systematically. In this study, we identified 30 genes that belonged to the KH family based on HMM of the KH domain in Arabidopsis thaliana. Phylogenetic tree analysis showed that the KH family is grouped into three subgroups. Synteny analysis showed that AtKH9 and AtKH29 have the conserved synteny relationship between A. thaliana and the other five species. The AtKH9 and AtKH29 were located in the cytoplasm and nucleus. The seed germination rates of the mutants atkh9 and atkh29 were higher than wild-type after abscisic acid (ABA) and salicylic acid (SA) treatments. In addition, the expression of ABA-related genes, such as ABRE-binding factor 2 (ABF2), ABRE-binding factor 4 (ABF4), and delta 1-pyrroline-5-carboxylate synthase (P5CS), and an SA-related gene pathogenesis-related proteins b (PR1b) were downregulated after ABA and SA treatments, respectively. These results suggested that atkh9 and atkh29 mutants inhibit the effect of ABA and SA on seed germination. In conclusion, our results provide valuable information for further exploration of the function of KH family genes and propose directions and ideas for the identification and characterization of KH family genes in other plants.

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Stewart, Lucy C., Jong-Hyun Jung, You-Tae Kim, Soon-Wo Kwon, Cheon-Seok Park, and James F. Holden. "M ethanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent." International Journal of Systematic and Evolutionary Microbiology 65, Pt_4 (April 1, 2015): 1280–83. http://dx.doi.org/10.1099/ijs.0.000097.

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A hyperthermophilic methanogen, strain JH146T, was isolated from 26 °C hydrothermal vent fluid emanating from a crack in basaltic rock at Marker 113 vent, Axial Seamount in the northeastern Pacific Ocean. It was identified as an obligate anaerobe that uses only H2 and CO2 for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is more than 97 % similar to other species of the genus Methanocaldococcus . Therefore, overall genome relatedness index analyses were performed to establish that strain JH146T represents a novel species. For each analysis, strain JH146T was most similar to Methanocaldococcus sp. FS406-22, which can fix N2 and also comes from Marker 113 vent. However, strain JH146T differs from strain FS406-22 in that it cannot fix N2. The average nucleotide identity score for strain JH146T was 87 %, the genome-to-genome direct comparison score was 33–55 % and the species identification score was 93 %. For each analysis, strain JH146T was below the species delineation cut-off. Full-genome gene synteny analysis showed that strain JH146T and strain FS406-22 have 97 % genome synteny, but strain JH146T was missing the operons necessary for N2 fixation and assimilatory nitrate reduction that are present in strain FS406-22. Based on its whole genome sequence, strain JH146T is suggested to represent a novel species of the genus Methanocaldococcus for which the name Methanocaldococcus bathoardescens is proposed. The type strain is JH146T ( = DSM 27223T = KACC 18232T).

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40

Berger, Bernard, R. David Pridmore, Caroline Barretto, Françoise Delmas-Julien, Kerstin Schreiber, Fabrizio Arigoni, and Harald Brüssow. "Similarity and Differences in the Lactobacillus acidophilus Group Identified by Polyphasic Analysis and Comparative Genomics." Journal of Bacteriology 189, no. 4 (December 1, 2006): 1311–21. http://dx.doi.org/10.1128/jb.01393-06.

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ABSTRACT A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the Lactobacillus acidophilus complex. On microarray analysis, 17 and 5% of the genes from Lactobacillus johnsonii strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of L. johnsonii. When projected on the NCC533 genome map, about 10 large clusters of variable genes were identified, and they were enriched around the terminus of replication. A quarter of the variable genes and two-thirds of the strain-specific genes were associated with mobile DNA. Signatures for horizontal gene transfer and modular evolution were found in prophages and in DNA from the exopolysaccharide biosynthesis cluster. On microarray hybridizations, Lactobacillus gasseri strains showed a shift to significantly lower fluorescence intensities than the L. johnsonii test strains, and only genes encoding very conserved cellular functions from L. acidophilus hybridized to the L. johnsonii array. In-silico comparative genomics showed extensive protein sequence similarity and genome synteny of L. johnsonii with L. gasseri, L. acidophilus, and Lactobacillus delbrueckii; moderate synteny with Lactobacillus casei; and scattered X-type sharing of protein sequence identity with the other sequenced lactobacilli. The observation of a stepwise decrease in similarity between the members of the L. acidophilus group suggests a strong element of vertical evolution in a natural phylogenetic group. Modern whole-genome-based techniques are thus a useful adjunct to the clarification of taxonomical relationships in problematic bacterial groups.

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Dolby, Greer A., Matheo Morales, Timothy H. Webster, Dale F. DeNardo, Melissa A. Wilson, and Kenro Kusumi. "Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds." Genome Biology and Evolution 12, no. 2 (February 1, 2020): 3917–25. http://dx.doi.org/10.1093/gbe/evaa016.

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Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

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Ramírez, Daniel, María Esther Rodríguez, Ismael Cross, Alberto Arias-Pérez, Manuel Alejandro Merlo, Marco Anaya, Silvia Portela-Bens, et al. "Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis." International Journal of Molecular Sciences 23, no. 10 (May 11, 2022): 5353. http://dx.doi.org/10.3390/ijms23105353.

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The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.

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Klockgether, Jens, Oleg Reva, Karen Larbig, and Burkhard Tümmler. "Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C." Journal of Bacteriology 186, no. 2 (January 15, 2004): 518–34. http://dx.doi.org/10.1128/jb.186.2.518-534.2004.

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ABSTRACT The Pseudomonas aeruginosa plasmid pKLC102 coexists as a plasmid and a genome island in clone C strains. Whereas the related plasmid pKLK106 reversibly recombines with P. aeruginosa clone K chromosomes at one of the two tRNALys genes, pKLC102 is incorporated into the tRNALys gene only close to the pilA locus. Targeting of the other tRNALys copy in the chromosome is blocked by a 23,395-bp mosaic of truncated PAO open reading frames, transposons, and pKLC102 homologs. Annotation and phylogenetic analysis of the large 103,532-bp pKLC102 sequence revealed that pKLC102 is a hybrid of plasmid and phage origin. The plasmid lineage conferred oriV and genes for replication, partitioning, and conjugation, including a pil cluster encoding type IV thin sex pili and an 8,524-bp chvB glucan synthetase gene that is known to be a major determinant for host tropism and virulence. The phage lineage conferred integrase, att, and a syntenic set of conserved hypothetical genes also observed in the tRNAGly-associated genome islands of P. aeruginosa clone C chromosomes. In subgroup C isolates from patients with cystic fibrosis, pKLC102 was irreversibly fixed into the chromosome by the insertion of the large 23,061-bp class I transposon TNCP23, which is a composite of plasmid, integron, and IS6100 elements. Intramolecular transposition of a copy of IS6100 led to chromosomal inversions and disruption of plasmid synteny. The case of pKLC102 in P. aeruginosa clone C documents the intraclonal evolution of a genome island from a mobile ancestor via a reversibly integrated state to irreversible incorporation and dissipation in the chromosome.

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Rehman, Shazia, Bodil Jørgensen, Ejaz Aziz, Riffat Batool, Samar Naseer, and Søren K. Rasmussen. "Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley." Plants 9, no. 11 (October 26, 2020): 1439. http://dx.doi.org/10.3390/plants9111439.

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Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

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Garrido-Bigotes, Adrián, Herman Silva, and Rodrigo Hasbún. "Genome-Wide Analysis of Somatic Embryogenesis-Related Transcription Factors in Cultivated Strawberry (Fragaria × ananassa) and Evolutionary Relationships among Rosaceae Species." Agronomy 11, no. 2 (February 17, 2021): 356. http://dx.doi.org/10.3390/agronomy11020356.

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Somatic embryogenesis is a plant regeneration method commonly used in tissue culture. Its molecular mechanisms are well-known in model plants such as Arabidopsis thaliana L. LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON2 (LEC2), FUSCA3 (FUS3), ABSCISIC ACID INSENSITIVE3 (ABI3), and BABYBOOM (BBM) genes are considered master regulators in the induction, growth, and maturation of somatic embryos. However, the study of these transcription factors in fruit crops with high agronomic and economic value such as cultivated strawberry (Fragaria × ananassa Duch.) and other Rosaceae species is scarce. The purpose of this study was the in silico characterization of LEC1, ABI3, FUS3, LEC2, and BBM(LAFL-B) genes from F. × ananassa genome and the study of the evolutionary relationships within the Rosaceae family. Synteny analyses and molecular evolutionary rates were performed to analyze the evolution of each transcription factor within the Rosaceae family. Synteny was conserved between F. × ananassa and other Rosaceae genomes, and paralogous genes were selected through negative selection. Additionally, the exon–intron organization and multiple alignments showed that gene structure and DNA-binding domains were conserved in F. × ananassa transcription factors. Finally, phylogenetic trees showed close evolutionary relationships between F. × ananassa and its orthologous proteins in the Rosoideae subfamily. Overall, this research revealed novel insights in the LAFL-B network in F. × ananassa and other species of the Rosaceae family. These results provide useful in silico information and new resources for the establishment of more efficient propagation systems or the study of ploidy effects on somatic embryogenesis.

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Maciel, Lucas, David Morales-Vicente, and Sergio Verjovski-Almeida. "Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum." Non-Coding RNA 6, no. 2 (April 1, 2020): 15. http://dx.doi.org/10.3390/ncrna6020015.

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Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification of protein-coding genes and pathways, whose expression levels were related to sexual development. However, this work did not include an analysis of long non-coding RNAs (lncRNAs). Here, we applied a pipeline to identify and annotate lncRNAs in 66 S. japonicum RNA-Seq publicly available libraries, from different life-cycle stages. We also performed co-expression analyses to find stage-specific lncRNAs possibly related to sexual maturation. We identified 12,291 S. japonicum expressed lncRNAs. Sequence similarity search and synteny conservation indicated that some 14% of S. japonicum intergenic lncRNAs have synteny conservation with S. mansoni intergenic lncRNAs. Co-expression analyses showed that lncRNAs and protein-coding genes in S. japonicum males and females have a dynamic co-expression throughout sexual maturation, showing differential expression between the sexes; the protein-coding genes were related to the nervous system development, lipid and drug metabolism, and overall parasite survival. Co-expression pattern suggests that lncRNAs possibly regulate these processes or are regulated by the same activation program as that of protein-coding genes.

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47

Han, F., A. Kleinhofs, S. E. Ullrich, A. Kilian, M. Yano, and T. Sasaki. "Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions." Genome 41, no. 3 (1998): 373–80. http://dx.doi.org/10.1139/gen-41-3-373.

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48

Hui, Jerome H. L., Peter W. H. Holland, and David E. K. Ferrier. "Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster." Evolution & Development 10, no. 6 (October 27, 2008): 725–30. http://dx.doi.org/10.1111/j.1525-142x.2008.00286.x.

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Yu, Jiajie, Xiang Zhang, Jiayu Cao, Heming Bai, Ruiqi Wang, Chao Wang, Zhiru Xu, Chunming Li, and Guanjun Liu. "Genome-Wide Identification and Characterization of WRKY Transcription Factors in Betula platyphylla Suk. and Their Responses to Abiotic Stresses." International Journal of Molecular Sciences 24, no. 19 (October 8, 2023): 15000. http://dx.doi.org/10.3390/ijms241915000.

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The WRKY transcription factor (TF) family is one the largest plant-specific transcription factor families. It has been proven to play significant roles in multiple plant biological processes, especially stress response. Although many WRKY TFs have been identified in various plant species, WRKYs in white birch (Betula platyphylla Suk.) remain to be studied. Here, we identified a total of 68 BpWRKYs, which could be classified into four main groups. The basic physiochemical properties of these TFs were analyzed using bioinformatics tools, including molecular weight, isoelectric point, chromosome location, and predicted subcellular localization. Most BpWRKYs were predicted to be located in the nucleus. Synteny analysis found 17 syntenic gene pairs among BpWRKYs and 52 syntenic gene pairs between BpWRKYs and AtWRKYs. The cis-acting elements in the promoters of BpWRKYs could be enriched in multiple plant biological processes, including stress response, hormone response, growth and development, and binding sites. Tissue-specific expression analysis using qRT-PCR showed that most BpWRKYs exhibited highest expression levels in the root. After ABA, salt (NaCl), or cold treatment, different BpWRKYs showed different expression patterns at different treatment times. Furthermore, the results of the Y2H assay proved the interaction between BpWRKY17 and a cold-responsive TF, BpCBF7. By transient expression assay, BpWRKY17 and BpWRKY67 were localized in the nucleus, consistent with the previous prediction. Our study hopes to shed light for research on WRKY TFs and plant stress response.

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Foote, Tracie, Michael Roberts, Nori Kurata, Takuji Sasaki, and Graham Moore. "Detailed Comparative Mapping of Cereal Chromosome Regions Corresponding to the Ph1 Locus in Wheat." Genetics 147, no. 2 (October 1, 1997): 801–7. http://dx.doi.org/10.1093/genetics/147.2.801.

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Detailed physical mapping of markers from rice chromosome 9, and from syntenous (at the genetic level) regions of other cereal genomes, has resulted in rice yeast artificial chromosome (YAC) contigs spanning parts of rice 9. This physical mapping, together with comparative genetic mapping, has demonstrated that synteny has been largely maintained between the genomes of several cereals at the level of contiged YACs. Markers located in one region of rice chromosome 9 encompassed by the YAC contigs have exhibited restriction fragment length polymorphism (RFLP) using deletion lines for the Ph1 locus. This has allowed demarcation of the region of rice chromosome 9 syntenous with the ph1b and ph1c deletions in wheat chromosome 5B. A group of probes located in wheat homoeologous group 5 and barley chromosome 5H, however, have synteny with rice chromosomes other than 9. This suggests that the usefulness of comparative trait analysis and of the rice genome as a tool to facilitate gene isolation will differ from one region to the next, and implies that the rice genome is more ancestral in structure than those of the Triticeae.

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