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红尾蚺和原矛头蝮基因组中微卫星分布的比较
Comparative Analysis of Microsatellite Distributions in Genomes of Boa constrictor and Protobothrops mucrosquamatus
聂虎,曹莎莎,赵明朗,杜林方*
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作者单位:四川大学生命科学学院生物资源与生物环境重点实验室
中文关键字:红尾蚺;原矛头蝮;基因组微卫星;密度分布
英文关键字:Boa constrictor; Protobothrops mucrosquamatus; genomic microsatellites; density distribution
中文摘要:本研究比较分析了红尾蚺和原矛头蝮基因组完美型微卫星的分布特征,通过MISA工具分别鉴定出398 860个和422 364个微卫星,其总长分别是8 550 741 bp和12 243 226 bp,分别占基因组大小的0.59%和0.73%,在各自基因组中的丰度分别为275.46个/Mbp和252.33个/Mbp。红尾蚺基因组中单碱基重复类型微卫星最多,其次是四碱基、二碱基、三碱基、五碱基和六碱基,最丰富的5种微卫星类型是A、AC、AAAT、AG、AAT;原矛头蝮基因组中单碱基重复类型的微卫星最多,其次是三碱基、四碱基、二碱基、五碱基和六碱基,最丰富的5种微卫星类型是A、AAT、AC、C、AAAT。红尾蚺和原矛头蝮微卫星在基因组不同区域丰度不同,基因间区丰度最高,其次是内含子区和外显子区,编码区微卫星丰度最低,这些现象表明编码区微卫星受到的选择压力最大。红尾蚺和原矛头蝮在基因区微卫星密度分布的位置特征相似,即微卫星在基因上下游500 bp密度最高,在内含子区次之,在外显子区密度最低。红尾蚺和原矛头蝮基因编码区所有六种重复类型的微卫星中,三碱基重复类型的微卫星占绝对优势。红尾蚺和原矛头蝮基因组中包含微卫星的编码序列分别有1 480条和1 397条,被GO注释的分别有736条和733条。它们的GO功能归类结果类似,但是和其他物种相比存在种系差异性。本研究结果为后续开发2种蛇类高质量微卫星标记提供了方便,也为进一步探索这些微卫星在它们基因组中的生物学功能提供了有意义的基础数据。
英文摘要: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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国内统一连续出版物号:51-1193/Q |国际标准出版物号:1000-7083
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