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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
Address:College of Life Sciences, Sichuan University, No.29, Wangjiang Road, Chengdu, Sichuan Province, 610064, China
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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-resource and Eco-environment of Ministry of Education. College of Life Sciences,Sichuan University
Key Words:Boa constrictor; Protobothrops mucrosquamatus; genomic microsatellites; density 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 Boa constrictor and Protobothrops mucrosquamatus, respectively. The total length of the identified microsatellites was 8,550,741 bp in Boa constrictor and 12,243,226 bp in Protobothrops mucrosquamatus, accounting for 0.59% and 0.73% of each genome respectively. The abundance of microsatellites was 275.46 no./Mbp in Boa constrictor and 252.33 no./Mbp in Protobothrops mucrosquamatus. In Boa 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 most abundant repeat units. In Protobothrops 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 most abundant repeat units. In both species, the abundances of microsatellites in intergenic region is the highest, followed by intron region and exon region, and the lowest is in coding region. These phenomena indicated that microsatellites in coding sequences were subject to the greatest selective pressure. The positional specificity of microsatellite density distributions in these two snakes were similar, that is, the density 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 six repeat units in the coding sequences of both genomes. The number of coding sequences containing microsatellites were 1,480 and 1,397, among which 736 and 733 were assigned with GO terms of known function in genomes of Boa constrictor and Protobothrops 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.
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