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Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
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Your Position :Home->Past Journals Catalog->2019 Vol.38 No.1

Characterization of Microsatellites in Phrynocephalus axillaris Genome Using Roche 454 GS FLX
Author of the article:SONG Qi1,2, LIU Jinlong1, GUO Xianguang1*
Author's Workplace:1. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China;
2. University of Chinese Academy of Sciences, Beijing 100049, China
Key Words:Phrynocephalus axillaris; genome; microsatellite; distribution
Abstract: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
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, 46(3): 185-191.
Allentoft ME, Schuster SC, Holdaway RN, et al. 2009. Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data[J]. Biotechniques, 46(3): 195-200.
Du LM, Zhang C, Liu Q, et al. 2018. Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design[J]. Bioinformatics, 34(4): 681-683.
Guichoux E, Lagache L, Wagner S, et al. 2011. Current trends in microsatellite genotyping[J]. Molecular Ecology Resources, 11(4): 591-611.
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.
Kim TS, Booth JG, Gauch HG, et al. 2008. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference[J]. BMC Genomics, 9(1): 31.
Nie H, Wu YY, Qiao L, et al. 2015. Development of novel microsatellite DNA markers for toad-headed agama Phrynocephalus vlangalii using next generation sequencing[J]. Conservation Genetics Resources, 7(2): 385-388.
Powell W, Machray GC, Provan J. 1996. Polymorphism revealed by simple sequence repeats[J].Trends in Plant Science, 1(7): 215-222.
Roche. 2011. 454 sequencing system software manual version 2.6. Part C: GS de novo assembler, GS reference mapper, SFF tools: Roche[M]. Branford, Connecticut: 454 Life Sciences Corporation.
Skinner DM, Beattie WG, Blattner FR, et al. 1974. The repeat sequence of a hermit crab satellite deoxyribonucleic acid is (-T-A-G-G-)n·(-A-T-C-C-)n[J]. Biochemistry, 13(19): 3930-3937.
Song N, Chen M, Gao T, et al. 2017. Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing[J]. Journal of Oceanology and Limnology, 35(1): 198-202.
Sun XY, Liu YD, Lutterbaugh J,et al. 2006. Detection of mononucleotide repeat sequence alterations in a large background of normal DNA for screening high-frequency microsatellite instability cancers[J]. Clinical Cancer Research, 12(2): 454-459.
Tóth G, Gáspári Z, Jurka J. 2000. Microsatellites in different eukaryotic genomes: survey and analysis[J].Genome Research, 10(7): 967-981.
Wierdl M, Dominska M, Petes TD. 1997. Microsatellite instability in yeast: dependence on the length of the microsatellite[J]. Genetics, 146(3): 769-779.
Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation: a review[J].Molecular Ecology, 11(1): 1-16.
Zhang Q, Xia L, He J, et al. 2010. Comparison of phylogeographic structure and population history of two Phrynocephalus species in the Tarim Basin and adjacent areas[J]. Molecular Phylogenetics and Evolution, 57(3): 1091-1104.
Zhou Q, Luo D, Ma L, et al. 2016. Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing[J]. Scientific Reports, 6: 20549.
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