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Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
Sponsored by:Sichuan Society of Zoologists; Chengdu Giant Panda Breeding Research Foundation; Sichuan Association of Wildlife Conservation; Sichuan University
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Your Position :Home->Past Journals Catalog->2017 Vol.36 No.6

Comparative Analysis of Microsatellite Distributions in Genomes of Boa constrictor and Protobothrops mucrosquamatus
Author of the article:NIE Hu, CAO Shasha, ZHAO Minglang, DU Linfang*
Author's Workplace:Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
Key Words:Boa constrictor; Protobothrops mucrosquamatus; genomic microsatellites; abundance distribution
Abstract:In this study, we analyzed and compared the distributions of perfect microsatellites in the genomes of Boa constrictor and Protobothrops mucrosquamatus. Using the MISA tool, a total of 398 860 and 422 364 microsatellites were identified in genomes of B. constrictor and P. mucrosquamatus, respectively. The total length of the identified microsatellites was 8 550 741 bp in B. constrictor and 12 243 226 bp in P. mucrosquamatus, accounting for 0.59% and 0.73% of each genome, respectively. The abundance of microsatellites was 275.46 no./Mbp in B. constrictor and 252.33 no./Mbp in P. mucrosquamatus. In B. constrictor genome, mono-nucleotide repeat was the most abundant, followed by tetra-nucleotide, di-nucleotide, tri-nucleotide, penta-nucleotide and hexa-nucleotide repeat, and A、AC、AAAT、AG、AAT were the 5 most abundant repeat units. In P. mucrosquamatus genome, mono-nucleotide repeat was the most abundant, followed by tri-nucleotide, tetra-nucleotide, di-nucleotide, penta-nucleotide and hexa-nucleotide, and A、AAT、AC、C、AAAT were the 5 most abundant repeat units. In both species, the abundances of microsatellites in intergenic region was the highest, followed by intron region and exon region, and the lowest was in coding region. These phenomena indicated that microsatellites in coding sequences were subject to the greatest selective pressure. The positional specificity of microsatellite abundance distributions in these 2 snakes were similar, that is, the abundance of microsatellites was the highest in the upstream and downstream 500 bp regions of genes, followed by intron regions and exon regions. Tri-nucleotide repeat was dominant among the 6 repeat units in the coding sequences of both genomes. The number of coding sequences containing microsatellites were 1 480 and1 397, among which 736 and 733 were assigned with GO terms of known function in genomes of B. constrictor and P. mucrosquamatus, respectively. These coding sequences resulted the similar GO classification outputs, but behaved in a lineage manner comparing with other species. This study made a great convenience to develop large number of high-quality microsatellite markers for these two snakes and provided meaningful underlying data for further exploration of the biological function of microsatellites in their genomes.
2017,36(6): 639-648 收稿日期:2017-03-08
高焕, 刘萍, 孟宪红, 等. 2004. 中国对虾(Fenneropenaeus chinensis)基因组微卫星特征分析[J]. 海洋与湖沼, 35(5):249-254.
李成云, 李进斌, 周晓罡, 等. 2004. 粗糙脉孢菌基因组中的微卫星序列的组成和分布[J]. 中国农业科学, 37(6):851-858.
李午佼, 李玉芝, 杜联明, 等. 2014. 大熊猫和北极熊基因组微卫星分布特征比较分析[J]. 四川动物, 33(6):874-878.
魏朝明, 孔光耀, 廉振民, 等. 2007. 蜜蜂全基因组中微卫星的丰度及其分布[J]. 昆虫知识, 44(4):501-504.
Conesa A, Götz S, García-Gómez JM, et al. 2005. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research[J]. Bioinformatics, 21(18):3674-3676.
Fujimori S, Washio T, Higo K, et al. 2003. A novel feature of microsatellites in plants:a distribution gradient along the direction of transcription[J]. FEBS Letters, 554(1):17-22.
Jurka J, Pethiyagoda C. 1995. Simple repetitive DNA sequences from primates:compilation and analysis[J]. Journal of Molecular Evolution, 40(2):120-126.
Kajitani R, Toshimoto K, Noguchi H, et al. 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads[J]. Genome Research, 24(8):1384-1395.
Kashi Y, King DG. 2006. Simple sequence repeats as advantageous mutators in evolution[J]. Trends in Genetics, 22(5):253-259.
Katti MV, Ranjekar PK, Gupta VS. 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences[J]. Molecular Biology and Evolution, 18(7):1161-1167.
Kerkkamp HM, Kini RM, Pospelov AS, et al. 2016. Snake genome sequencing:results and future prospects[J]. Toxins, 8(12):360-375.
Laurie JV, Janalee PC. 2009. Herpetology:an introduction biology of amphibians and reptiles (third edition)[M]. London:Academic Press:551-578.
Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL:identification of ortholog groups for eukaryotic genomes[J]. Genome Research, 13(9):2178-2189.
Li YC, Korol AB, Fahima T, et al. 2004. Microsatellites within genes:structure, function, and evolution[J]. Molecular Biology and Evolution, 21(6):991-1007.
Lin WH, Kussell E. 2012. Evolutionary pressures on simple sequence repeats in prokaryotic coding regions[J]. Nucleic Acids Research, 40(6):2399-2413.
Loire E, Higuet D, Netter P, et al. 2013. Evolution of coding microsatellites in primate genomes[J]. Genome Biology and Evolution, 5(2):283-295.
Reyes-Velasco J, Card DC, Andrew AL, et al. 2015. Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom[J]. Molecular Biology and Evolution, 32(1):173-183.
Thiel T, Michalek W, Varshney R, et al. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theoretical and Applied Genetics, 106(3):411-422.
Tóth G, Gáspári Z, Jurka J. 2000. Microsatellites in different eukaryotic genomes:survey and analysis[J]. Genome Research, 10(7):967-981.
Wang C, Kubiak L, Du L, et al. 2016. Comparison of microsatellite distribution in genomes of Centruroides exilicauda and Mesobuthus martensii[J]. Gene, 594(1):41-46.
Yin W, Wang Z, Li Q, et al. 2016. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper[J]. Nature Communications, 13107(7):1-11.
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