Latest Cover

Online Office

Contact Us

Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
Sponsored by:Sichuan Society of Zoologists; Chengdu Giant Panda Breeding Research Foundation; Sichuan Association of Wildlife Conservation; Sichuan University
Address:College of Life Sciences, Sichuan University, No.29, Wangjiang Road, Chengdu, Sichuan Province, 610064, China
Tel:+86-28-85410485
Fax:+86-28-85410485
Email:scdwzz@vip.163.com & scdwzz001@163.com
Your Position :Home->Past Journals Catalog->2016 Vol.35 No.1

Analysis of Microsatellite Composition in Paa boulengeri using RNA-seq
Author of the article:JIANG Yusong1, FAN Wenqiao1, XU Jingming2
Author's Workplace:1. College of Life Science & Forestry, Chongqing University of Art & Science, Chongqing 402160, China;
2. Chongqing Research Centers of Conservation & Development on Rare & Endangered Aquatic Resources, Chongqing 402168, China
Key Words:high-throughput sequencing; Paa boulengeri; microsatellite
Abstract:The genetic and genomic information of Paa boulengeri was relatively lacking, which have caused a limited number of effective DNA markers. Based on the RNA-seq database, microsatellite markers in P. boulengeri were analyzed by the Misa program. A total of 3165 microsatellite loci that occurred in 3034 Contig sequences were identified in a total of 121.6 Mb nucleotides. Mononucletide repeats was the major types, followed by the trinucleotide, dinucleotide, tetranucleotide, hexanucleoide and pentanucleotide, accounting for 29.0%, 25.2%, 21.7%, 10.0%, 10.0% and 3.0%, respectively. A/T, AC/GT, AGG/CCT, ACAT/ATCT, AAAAT/ATTTT and AAAAAG/CTTTTT were the most frequent motifs in mon-, din-, tri-, tetra-, penta- and hexa-nucleotide repeats, and all of them were rich in A or T. The average length of microsatellites in the coding region of P. boulengeri was 18-24 bp, and the length more than 24 bp only accounted for 0.92%. In addition, we found that the GC content of the flanking sequences was significantly lower than that of transcriptomic sequences. For the Contig sequences with paired flanking sequences longer than 50 nt, 71.9% of them contained the sequences corresponding to the predicted microsatellite loci as determined by PCR. These results provided abundant sequences and microsatellite markers for molecular phylogeography and genetic research on P. boulengeri.
2016,(1): 24-30 收稿日期:2015-04-24
DOI:10.11984/j.issn.1000-7083.20150147
分类号:Q78;Q959.5
基金项目:重庆文理学院人才引进项目(R2014LX07,R2013LS13); 重庆市前沿与应用基础研究(一般)项目(cstc2014jcyjA80042); 重庆市科技攻关计划(cstc2012gg-yyjs80004)
作者简介:姜玉松(1984-), 博士, 讲师, 主要从事基因的分子生物学研究, E-mail:jysong@126.com
*通讯作者:徐敬明, 博士, 教授, 主要从事两栖动物的分子系统地理学研究, E-mail:proteomics@163.com
参考文献:
费梁, 叶昌媛, 江建平. 2005. 中国两栖动物检索及图解[M]. 成都: 四川科学技术出版社: 136-137.
廖小林, 俞小牧, 谭德清, 等. 2005. 长江水系草鱼遗传多样性的微卫星DNA分析[J]. 水生生物学报, 29: 113-119.
鲁翠云, 孙效文, 梁利群, 等. 2005. 鳙鱼微卫星分子标记的筛选[J]. 中国水产科学, 12(2): 192-196.
孙国华, 杨建敏, 宋志乐, 等. 2010. 刺参(Apostichopus japonicus) EST序列中微卫星分布分析及其标记的筛选[J]. 海洋与湖沼, 41(1): 133-138.
袁慧, 张修月, 宋昭彬. 2008. 岩原鲤微卫星富集文库的构建及微卫星分子标记的筛选[J]. 四川动物, 27(2): 210-215.
曾聪, 高泽霞, 罗伟, 等. 2013. 基于454 GSFLX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.
曾晓芸, 杨宗英, 田辉伍, 等. 2015. 基于Mi-Seq高通量测序分析裸体异鳔鳅微卫星组成[J]. 淡水渔业, 45(1): 3-7.
张琼, 刘小林, 李喜莲, 等. 2010. EST-SSR分子标记在水生动物遗传研究中的应用[J]. 水产科学, 29(5): 302-306.
赵尔宓, 张学文, 赵慧. 2000. 中国两栖纲和爬行纲动物校正名录[J]. 四川动物, 19(3): 196-207.
郑劲松, 廖小林, 童金苟, 等. 2008. 长江江豚微卫星DNA分离的初步研究[J]. 水生生物学报, 32(1): 19-25.
周小龙, 朱靖华,董迎辉, 等. 2013. 泥蚶(Tegillarca granosa)基因组SSR和EST-SSR的开发及比较研究[J]. 海洋与湖沼, 44(2): 467-475.[ZK)]
Chang YH, Su WH, Lee TC. 2005. TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations[J]. Nucleic Acids Research, 33: 174-177.
Garner TWJ. 2002. Genome size and microsatellites: the effect of nuclear size on amplification potential[J]. Genome, 45: 212-215.
Jehle R, Arntzen JW. 2002. Review: microsatellite markers in amphibian conservation genetics[J]. Herpetological Journal, 12: 1-9.
Kijas JMH, Fowler JCS, Garbett CA, et al. 1994. Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles[J]. Biotechnology Techniques, 16: 656-662.
Kijas JMH, Thomas MR, Fowler JCS. 1997. Integration of trinucleotide microsatellites into a linkage map of Citrus[J]. Theoretical and Applied Genetics, 94(5): 701-706.
Kofler R, Schlotterer C, Luschutzky E, et al. 2008. Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites[J]. BMC Genomics, 9(1): 612.
Mrazek J, Guo X, Shah A. 2007. Simple sequence repeats in prokaryotic genomes[J]. Proceedings of the National Academy of Sciences of the United States of America, 104: 8472-8477.
Oyamaguchi HM, Okubo RP, Pollinger JP. 2015. Characterization of new polymorphic microsatellite loci for the lesser tree frog (Dendropsophus minutus)[J]. Amphibia-Reptilia, 36(1): 83-86.
Rowe G, Beebee TJC, Burke T. 2000. A microsatellite analysis of natterjack toad, Bufo calamita, metapopulations[J]. Oikos, 88: 85-92.
Samadi S, Artiguebielle E, Estoup A, et al. 1998. Density and variability of dinucleotide microsatellites in the parthenogenetic polyploid snail Melanoides tuberculata[J]. Molecular Ecology, 7(9): 1233-1236.
Tong J, Wang ZW, Wu QJ, et al. 2002. Cross-species amplification in silver carp and big head carp with microsatellite primers of common carp[J]. Molecular Ecology Notes, 2: 245-248.
Wang C, Hu X, Xie X, et al. 2013. Isolation and characterization of 113 polymorphic microsatellite loci for the Tibetan frog (Nanorana parkeri) using next generation sequencing[J]. Conservation Genetics Resources, 5(4): 915-924.
Weber JL. 1990. In formativeness of human (dC-dA)n(dG-dT)n polymorphisms[J]. Genomics, 7: 524-530.
Yuan SQ, Xia Y, Zheng YC, et al. 2015. Development of microsatellite markers for the spiny-bellied frog Quasipaa boulengeri (Anura: Dicroglossidae) through transcriptome sequencing[J]. Conservation Genetics Resources, 7(1): 229-231.
Zheng K, Lin KD, Liu ZH, et al. 2007. Comparative microsatellite analysis of grass carp genomes of two gynogenetic groups and the Xiangjiang River Group[J]. Journal of Genetics and Genomics, 34(4): 321-330.
CopyRight©2022 Editorial Office of Sichuan Journal of Zoology 蜀ICP备08107403号-3