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绿尾虹雉全基因组微卫星分布规律研究
Distribution Patterns of Microsatellites in the Genome of Lophophorus lhuysii
崔凯, 岳碧松*
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作者单位:四川大学生命科学学院, 生物资源与生态环境教育部重点实验室, 成都 610065
中文关键字:绿尾虹雉;基因组;微卫星
英文关键字:Lophophorus lhuysii; genome; microsatellite
中文摘要:分析了绿尾虹雉Lophophorus lhuysii全基因组中微卫星的数量和分布规律,并对外显子中含有微卫星的基因进行了注释分析。结果显示,在绿尾虹雉1.01 Gb的全基因组中,1~6个碱基重复类型的完美型微卫星序列共292 430个,总长度5 465 549 bp,相对丰度为290.47个/Mb,占全基因组的0.54%,序列长度主要为10~43 bp。不同类型的微卫星中,单碱基重复类型数量最多,长度为3 535 260 bp,占71.75%,其次是四碱基(611 568 bp,9.99%)、二碱基(376 944 bp,7.07%)、三碱基(335 742 bp,6.38%)、五碱基(500 615 bp,3.93%)和六碱基(105 420 bp,0.88%)重复类型。在绿尾虹雉全基因组中,数目最多的10种优势微卫星分别是:A、C、AAAC、AT、AAAT、AC、AAT、AAC、AG、AAAAC,共计占90.20%,表现出明显A偏倚。分布于外显子的微卫星有2 816个,内含子的有101 791个,基因间区的有187 823个。外显子的微卫星分布于1 314个编码基因中。GO注释分析发现,这些编码基因主要与细胞组分有关,富集前10的条目主要与代谢、转录和合成过程有关。KEGG富集最显著的通路是黏着连接通路。位于外显子的微卫星移码突变可能会造成基因突变,进而可能会影响绿尾虹雉对环境信号的处理。本研究为绿尾虹雉的微卫星筛选和进一步的遗传多样性、功能研究提供了数据基础,从分子角度为绿尾虹雉的保护提供了基础信息。
英文摘要:In this study, the quantity and distribution of genome-wide microsatellites in the Chinese monal (Lophophorus lhuysii) were analyzed, and the coding genes containing microsatellites were annotated. The results showed that in the whole genome of L. lhuysii (1.01 Gb), there were 29·2 430 perfect microsatellite sequences of bases 1-6 with a total length of 5 465 549 bp and relative abundance of 290.47 loci/Mb, accounting for 0.54% of the whole genome sequence. The microsatellite sequence length was mainly between 10-43 bp. Among the different types of microsatellites, mononucleotide microsatellites (3 535 260 bp, 71.75%) were the most abundant simple sequence repeats (SSRs), and the lengths of other types of microsatellites were much smaller than the mononucleotide type. The other microsatellites were tetranucleotide (611 568 bp, 9.99%), dinucleotide (376 944 bp, 7.07%), trinucleotide (335 742 bp, 6.38%), pentanucleotide (500 615 bp, 3.93%) and hexanucleotide (105 420 bp, 0.88%). The top 10 dominant microsatellites in L. lhuysii genome were A, C, AAAC, AT, AAAT, AC, AAT, AAC, AG and AAAAC, accounting for 90.20% of the SSRs and showing an obvious A bias. The number of microsatellites located on the exon region was 2 816, and was significantly less than that on the 101 791 non-coding sequences and 187 823 intergenic regions. The genes (n=1 314) in which the microsatellites were distributed in the exon region were annotated. GO annotation analysis showed that these genes were mainly related to cellular components and the top 10 enriched terms were predominantly related to metabolism, synthesis process and transcription. The most enriched KEGG pathway was related to adherens junction. The microsatellites in the exon likely cause genetic mutations. The microsatellites distributed in the exon region were found to be associated with environmental information processing, cellular basic component and metabolism. Any mutations in this location might affect the ability of L. lhuysii to adapt to environmental stimulation and fluctuations. This study provides basic data for the further study of microsatellite and genetic diversity in L. lhuysii, and provides useful information for the protection of L. lhuysii.
2018,37(5): 533-540 收稿日期:2018-03-22
DOI:10.11984/j.issn.1000-7083.20180096
分类号:Q959.7;R857.3
基金项目:珍稀动物濒危机制及保护技术研究项目(2016YFC0503200)
作者简介:崔凯,女,硕士研究生,主要从事动物基因组和转录组分析研究工作,E-mail:katecuikai@gmail.com
*通讯作者:岳碧松,E-mail:bsyue@scu.edu.cn
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