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Your Position :Home->Past Journals Catalog->2019 Vol.38 No.5

Characterization of Microsatellite DNA Loci and Design of Candidate Primers to Amplify These Regions for Phrynocephalus forsythii by Using 454 GS FLX
Author of the article:SONG Qi1,2, GUO Xianguang1, CHEN Dali3*
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;
3. West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610064, China
Key Words:Phrynocephalus forsythii; genome; microsatellite; distribution; primer sequence
Abstract:The Forsyth's toad-headed agama, Phrynocephalus forsythii, is an endemic small lizard in the Tarim Basin in northwest China. The genome data of P. forsythii was generated using Roche 454 sequencing platform, and 55 909 high quality sequences were obtained. A total of 12 109 simple sequence repeats (SSRs) with 1-6 bp nucleotide motifs were identified by using Krait. Among the different repeat types of screened microsatellite DNA, tetranucleotide, having 4 037 (33.34%), was the most common repeat unit followed by the di-(28.09%), tri-(18.72%), mono-(13.91%), penta-(4.48%) and hexanucleotides (1.46%). Additionally, C, AC, AAC, AAAT, AAAAT, and AACCCT were the most common repeat units among the mono-hexanucleotides, respectively. In the genome of P. forsythii, there were 10 predominant repeat types, including AC, AAAT, C, AG, A, AAC, AAT, AAAC, ACC and ACG. One hundred pairs of candidate primers containing a part of tri-and tetranucleotide repeat types were designed to amplify the microsatellite DNA loci in P. forsythii. This study sheds new light on understanding the feature of genomic microsatellite DNA in P. forsythii, and lays a foundation for further studying the population genetic structure of P. forsythii by using microsatellite markers.
2019,38(5): 512-520 收稿日期:2019-01-09
分类号:Q959.6;R857.3
基金项目:国家自然科学基金项目(31672270,31872959);科技部重点研发计划项目(2017YFC0505202)
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:陈达丽,E-mail:cdl1978119@sina.com
参考文献:
崔凯, 岳碧松. 2018. 绿尾虹雉全基因组微卫星分布规律研究[J]. 四川动物, 37(5):533-540.
戴昆, 马鸣. 1991. 新疆南部三种沙蜥对山地及荒漠的适应性初报[J]. 干旱区研究, 8(1):47-49.
高焕, 刘萍, 孟宪红, 等. 2004. 中国对虾(Fenneropenaeus chinensis)基因组微卫星特征分析[J]. 海洋与湖沼, 35(5):424-431.
黄杰, 杜联明, 李玉芝, 等. 2012. 红原鸡全基因组中微卫星分布规律研究[J]. 四川动物, 31(3):358-363.
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.
廖卓毅, 马秋月, 戴晓港, 等. 2014. 利用高通量测序技术分析核桃基因组微卫星特征[J]. 东北林业大学学报, 42(2):65-68, 82.
马秋月, 戴晓港, 陈赢男, 等. 2013. 枣基因组的微卫星特征[J]. 林业科学, 49(12):81-87.
聂虎, 曹莎莎, 赵明朗, 等. 2017. 红尾蚺和原矛头蝮基因组微卫星分布特征比较分析[J]. 四川动物, 36(6):639-648.
戚文华, 蒋雪梅, 肖国生, 等. 2013. 牛和绵羊全基因组微卫星序列的搜索及其生物信息学分析[J]. 畜牧兽医学报, 44(11):1724-1733.
汪自立, 黄杰, 杜联明, 等. 2013. 二斑叶螨和肩突硬蜱基因组微卫星分布规律研究[J]. 四川动物, 32(4):481-486.
魏朝明, 孔光耀, 廉振民, 等. 2007. 蜜蜂全基因组中微卫星的丰度及其分布[J]. 应用昆虫学报, 44(4):501-504.
吾玛尔·阿布力孜, 杨立中. 1999. 南疆沙蜥精巢的显微结构观察[J]. 新疆大学学报(自然科学版), 16(2):52-57.
吾玛尔·阿布力孜, 于甫尔·米吉提, 杨立中. 2000. 南疆沙蜥受精过程的细胞学研究[J]. 新疆大学学报(自然科学版), 17(2):69-73.
曾晓茂, 王跃招, 刘志君, 等. 1997. 九种沙蜥的核型——兼论中国沙蜥属核型演化[J]. 动物学报, 43(4):399-410.
Allentoft M, Schuster SC, Holdaway R, et al. 2009. Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data[J]. Biotechniques, 46(3):195-200.
Chen DL, Li J, Guo XG. 2019. Next-generation sequencing yields a nearly complete mitochondrial genome of the Forsyth's toad-headed agama, Phrynocephalus forsythii (Reptilia, Squamata, Agamidae)[J]. Mitochondrial DNA Part B, 4(1):817-819.
Chen DL, Zhou T, Guo XG. 2016. The complete mitochondrial genome of Phrynocephalus forsythii (Reptilia, Squamata, Agamidae), a toad-headed agama endemic to the Taklamakan Desert[J]. Mitochondrial DNA, 27(6):4046-4048.
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.
Goldstein DB, Clark AG. 1995. Microsatellite variation in North American populations of Drosophila melanogaster[J]. Nucleic Acids Research, 23(19):3882-3886.
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.
Nie H, Wu Y, 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.
O'connell M, Wright JM. 1997. Microsatellite DNA in fishes[J]. Reviews in Fish Biology and Fisheries, 7(3):331-363.
O'reilly P, Wright JM. 1995. The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture[J]. Journal of Fish Biology, 47(sA):29-55.
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.
Schlötterer C, Ritter R, Harr B, et al. 1998. High mutation rate of a long microsatellite allele in Drosophila melanogaster provides evidence for allele-specific mutation rates[J]. Molecular Biology & Evolution, 15(10):1269-1274.
Schlötterer C. 2000. Evolutionary dynamics of microsatellite DNA[J]. Chromosoma, 109(6):365-371.
Selkoe KA, Toonen RJ. 2006. Microsatellites for ecologists:a practical guide to using and evaluating microsatellite markers[J]. Ecology Letters, 9(5):615-629.
Shao M, Ma L, Wang Z. 2016. The complete mitochondrial genome of the toad-headed lizard, Phrynocephalus forsythii (Reptilia, Squamata, Agamidae)[J]. Mitochondrial DNA Part A, 27(5):3147-3148.
Tóth G, Gáspári Z, Jurka J. 2000. Microsatellites in different eukaryotic genomes:survey and analysis[J]. Genome Research, 10(7):967-981.
Weber JL, Wong C. 1993. Mutation of human short tandem repeats[J]. Human Molecular Genetics, 2(8):1123-1128.
Wierdl M, Dominska M, Petes TD. 1997. Microsatellite instability in yeast:dependence on the length of the microsatellite[J]. Genetics, 146(3):769-777.
Xia Y, Luo W, Yuan S, et al. 2018. Microsatellite development from genome skimming and transcriptome sequencing:comparison of strategies and lessons from frog species[J]. BMC Genomics, 19(1):886. DOI:10.1186/s12864-018-5329-y.
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.
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