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基于Roche 454 GS FLX高通量测序的叶城沙蜥基因组微卫星特征分析
Characterization of Microsatellites in Phrynocephalus axillaris Genome Using Roche 454 GS FLX

DOI: 10.11984/j.issn.1000-7083.20180264

Keywords: 叶城沙蜥,基因组序列,微卫星,分布
英文关键字: Phrynocephalus axillaris
, genome, microsatellite, distribution

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中文摘要:叶城沙蜥 Phrynocephalus axillaris是我国特有的一种小型爬行动物,广泛分布于新疆塔里木盆地、吐鲁番-哈密盆地和甘肃敦煌盆地。本研究利用Roche 454 GS FLX高通量测序技术进行叶城沙蜥微卫星位点筛选,获得了91 190条高质量序列。用Krait搜索微卫星位点,共得到1~6个碱基重复类型的完美型微卫星序列29 890个。不同类型微卫星中,单碱基重复类型数目最多,有14 630个,占总数的48.95%,其次是二碱基,约占28.60%,四碱基、三碱基、五碱基和六碱基分别占10.73%、10.48%、0.92%和0.32%。二碱基微卫星中AC重复类型数量最多,三碱基、四碱基、五碱基和六碱基中分别是ATC、AAAT、AAAAT和AATCCC。叶城沙蜥完美型微卫星中数量最多的11种重复拷贝类型分别为C、A、AC、AG、AAAT、ATC、AT、AAT、ATAG、AGG和AAC。本研究深化了对叶城沙蜥基因组的了解,并为以后开发和筛选大量高质量微卫星标记提供了数据支持,也为利用微卫星标记研究叶城沙蜥种群遗传结构和谱系地理模式奠定了基础。
英文摘要:Yarkand toad-headed agama ( Phrynocephalus axillaris), a small reptile endemic to China, is widely distributed in Tarim Basin, Turpan-Hami Basin, Xinjiang Uygur Autonomous Region and Dunhuang Basin, Gansu province. The whole genome of P. axillaris was sequenced using Roche 454 GS FLX platform, and 91 190 high quality sequences were obtained. A total of 29 890 simple sequence repeats with 1-6 bp nucleotide motifs were identified by Krait. Among the different repeat types of the microsatellites, mononucleotide (48.95%) was the most common repeat unit, followed by the di- (28.60%), tetra- (10.73%), tri- (10.48%), penta- (0.92%) and hexanucleotides (0.32%). AC, ATC, AAAT, AAAAT, and AATCCC were the most common repeat units among the di-, tri-, tetra-, penta-, and hexanucleotides, respectively. In the genome of P. axillaris, there were 11 predomiant repeat types, which included C, A, AC, AG, AAAT, ATC, AT, AAT, ATAG, AGG and AAC. This study contributes to the understanding of the genetic feature for P. axillaris, and will provide data support for development and screening of high quality microsatellite markers. In addition, this study lays a foundation for further revealing the population genetic structure and phylogeographic pattern of this lizard using microsatellite markers. 2019,38(1): 62-67 收稿日期:2018-09-03 分类号:Q959.6;R857.3 基金项目:科技部重点研发计划项目(2017YFC0505202);国家自然科学基金项目(31672270) 作者简介:宋琪(1992—),女,硕士研究生,研究方向:分子进化与系统发育,E-mail:songqi@cib.ac.cn *通信作者:郭宪光,E-mail:guoxg@cib.ac.cn 参考文献: 程晓凤, 黄福江, 刘明典, 等. 2011. 454测序技术开发微卫星标记的研究进展[J]. 生物技术通报, 8: 82-90. 黄杰, 周瑜, 刘与之, 等. 2015. 基于454 GS FLX高通量测序的四川山鹧鸪基因组微卫星特征分析[J]. 四川动物, 34(1): 8-14. 李俊. 2013. 叶城沙蜥线粒体基因组特征及基于ND4基因的谱系地理研究[D]. 北京: 中国科学院大学. 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. 曾聪, 高泽霞, 罗伟, 等. 2013. 基于454 GS FLX高通量测序的团头鲂ESTs中微卫星特征分析[J]. 水生生物学报, 37(5): 982-988. 赵尔宓, 赵肯堂, 周开亚, 等. 1999. 中国动物志爬行纲(第二卷)有鳞目 蜥蜴亚目[M]. 北京: 科学出版社: 157-160. Abdelkrim J, Robertson BC, Stanton JAL, et al. 2009. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing[J]. Biotechniques,

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