刊期:双月刊
主管单位:四川省科学技术协会
主办单位:四川省动物学会/成都大熊猫繁育研究基金会/四川省野生动植物保护协会/四川大学
地址:四川省成都市武侯区望江路29号四川大学生命科学学院内
邮编:610064
电话:028-85410485; 15881112385
传真:028-85410485
E-Mail:scdwzz@vip.163.com & scdwzz001@163.com
刊号:ISSN 1000-7083
        CN 51-1193/Q
国内发行代号:
国际发行代号:
发行范围:国内外公开发布
定价:50元/册
定价:300元/年

您所在位置:首页->过刊浏览->2017年第36卷第4期

林麝全基因组微卫星分布规律研究
Distribution Regularity of Microsatellites in Moschus berezovskii Genome
卢婷1#, 王晨1#, 杜超1, 刘姝2, 沈咏梅2, 张修月1, 岳碧松1*
点击:326次 下载:0次
DOI:
作者单位:1. 四川大学生命科学学院, 四川省濒危野生动物保护生物学重点实验室, 成都 610064;
2. 四川省药用动物工程技术研究中心, 成都 610081
中文关键字:林麝;全基因组;微卫星;分布规律
英文关键字:Moschus berezovskii; genome; microsatellite; distribution regularities
中文摘要:林麝Moschus berezovskii是中国重要的资源动物,也是国家Ⅰ级重点保护野生动物。本研究使用生物信息学方法,分析林麝全基因组中完美型微卫星的分布特征。在林麝2.53 Gb的基因组序列中,共搜索到665 524个完美型微卫星,总长度为11 517 784 bp,占基因组序列总长度的0.42%,总丰度为244个/Mb。林麝基因组中,单碱基微卫星序列数量最多,为221 058个,约占总微卫星数的33.22%,丰度为81.05个/Mb,然后依次为二碱基、五碱基、三碱基、四碱基、六碱基重复类型微卫星。林麝基因组中数目最多的10种微卫星类别依次为:A、AACTG、AGC、AC、AT、AG、AAAT、AAC、AAT和AAAC,占所有基因组微卫星的93.2%,表现出明显的A、T偏好。林麝基因组微卫星序列分布研究表明,其在外显子(2 530个)上的分布数量远低于内含子(200 906个)和基因间隔区(454 596个),与前人关于微卫星在非编码区的分布多于编码区的结论一致。本研究为深入研究林麝基因组特征及筛选更多优良微卫星标记提供了基础数据。
英文摘要:Forest musk deer (Moschus berezovskii) is a critically endangered species. Perfect microsatellite number and distribution regularity of microsatellites in forest musk deer genome were analyzed by microsatellite search tool. A repertoire of 665 524 perfect SSRs with 1-6 bp nucleotide motifs accounting for 0.42% of forest musk deer genome (2.53 Gb) were scanned, and the abundance of microsatellites was 244 no./Mb. Mono-nucleotide was the most abundant category with the highest relative abundance (81.05 no./Mb), accounting for 33.22% of all the SSRs, followed by di-nucleotide (21.68%), pentra-nucleotide (21.09%), tri-nucleotide (18.08%), tetra-nucleotide (5.86%), and hexa-nucleotide (0.09%). The most abundant microsatellite repeats in forest musk deer genome were A, AACTG, AGC, AC, AT, AG, AAAT, AAC, AAT, and AAAC, totally accounting 93.2% of the scanned microsatellites and showed an apparent A and T preference. The number of microsatellites located on the coding sequences (n=2 530) was less than that on the non-coding sequence such as introns (n=200 906) and intergenic regions (n=454 596), and this was consistent with previous studies. This study provides adequate material for the future study of forest musk deer.
2017,36(4): 420-424 收稿日期:2017-02-17
DOI:10.11984/j.issn.1000-7083.20170044
分类号:Q959.8
基金项目:四川省科技支撑计划(2014NZ0107)
作者简介:卢婷(1991-),女,硕士研究生,从事动物分子生物学研究,E-mail:619016141@qq.com
*通讯作者:岳碧松,E-mail:bsyue@scu.edu.cn
参考文献:
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.
蒋雪梅, 胡廷章, 向兴胜, 等. 2015. 杨树全基因组微卫星序列的统计及其生物信息学分析[J]. 西南农业学报, 28(2):527-533.
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.
李玉芝. 2012. 大熊猫基因组微卫星序列分析和遗传标记筛选[D]. 成都:四川大学.
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.
戚文华, 蒋雪梅, 肖国生, 等. 2014. 猪全基因组中微卫星分布规律[J]. 畜牧与兽医, 46(8):9-13.
童晓玲, 代方银, 李斌, 等. 2006. 小鼠基因组中的微卫星重复序列的数量、分布和密度[J]. Current Zoology, 52(1):138-152.
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.
王月月, 刘雪雪, 董坤哲, 等. 2015. 7种家养动物全基因组微卫星分布的差异研究[J]. 中国畜牧兽医, 42(9):2418-2426.
王淯, 姜海瑞, 薛文杰, 等. 2006. 林麝(Moschus berezovskii)研究概况和进展[J]. 四川动物, 25(1):195-200.
许珂, 卜书海, 梁宗锁, 等. 2013. 林麝研究进展[J]. 黑龙江畜牧兽医, (7):147-150.
Archie EA, Moss CJ, Alberts SC. 2003. Characterization of tetranucleotide microsatellite loci in the African Savannah elephant (Loxodonta africana africana)[J]. Molecular Ecology Notes, 3(2):244-246.
Doyle JM, Siegmund G, Ruhl JD, et al. 2013. Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens,Ambystoma tigrinum, and Dipodomys spectabilis)[J]. Genome, 56:407-414.
Du LM, Li YZ, Zhang XY, et al. 2013. MSDB:a user-friendly program for reporting distribution and building databases of microsatellites from genome sequences[J]. Journal of Heredity, 104(1):154-157.
Ellegren H. 2000. Heterogeneous mutation processes in human microsatellite DNA sequences[J]. Nature Genetics, 24(4):400-402.
Ellegren H. 2004. Microsatellites:simple sequences with complex evolution[J]. Nature Reviews Genetics, 5(6):435-445.
Harr B, Schl tterer C. 2000. Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation[J]. Genetics, 155(3):1213-1220.
Huang J, Li YZ, Li P, et al. 2013. Genetic quality of the Miyaluo captive forest musk deer (Moschus berezovskii) population as assessed by microsatellite loci[J]. Biochemical Systematics & Ecology, 47(8):25-30.
Huang J, Li YZ, Du LM, et al. 2015. Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system[J]. BMC Genomics, 16(1):1-12.
Li YZ, Xu X, Shen FJ, et al. 2010. Development of new tetranucleotide microsatellite loci and assessment of genetic variation of giant panda in two largest giant panda captive breeding populations[J]. Journal of Zoology, 282(1):39-46.
Ma Z. 2015. Genome-wide characterization of perfect microsatellites in yak (Bos grunniens)[J]. Genetica, 143(4):1-6.
Massault C, Hellemans B, Louro B, et al. 2010. QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax[J]. Animal Genetics, 41(4):337-345.
Meng X, Zhou C, Hu J, et al. 2006. Musk deer farming in China[J]. Animal Science An International Journal of Fundamental & Applied Research, 82(1):1-6.
Metzgar D, Bytof J, Wills C. 2000. Selection against frameshift mutations limits microsatellite expansion in coding DNA[J]. Genome Research, 10(1):72-80.
Serbezov D, Bernatchez L, Olsen EM, et al. 2010. Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population[J]. Molecular Ecology, 19(15):3193-3205.
Sheng HL, Liu ZX. 2007. The musk deer in China[M]. Shanghai:The Shanghai Scientific & Technical Publishers.
Subramanian S, Mishra RK, Singh L. 2003. Genome-wide analysis of microsatellite repeats in humans:their abundance and density in specific genomic regions[J]. Genome Biology, 4(2):1-10.
Tautz D. 1989. Hyper variability of simple sequences as a general source for polymorphic DNA markers[J]. Nucleic Acids Research, 17(16):6463-6471.
Webster MT, Smith NGC, Ellegren H. 2002. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments[J]. Proceedings of the National Academy of Sciences of the United States of America, 99(13):8748-8753.
Wierdl M, Dominska M, Petes TD. 1997. Microsatellite instability in Yeast:dependence on the length of the microsatellite[J]. Genetics, 146(3):769-779.
Xia S, Zou FD, Yue BS. 2006. Six microsatellite loci in forest musk deer, Moschus berezovskii[J]. Molecular Ecology Notes, 6(1):113-115.
Zou F, Yue B, Liu X, et al. 2005. Isolation and characterization of microsatellite loci from forest musk deer (Moschus berezovskii)[J]. Zoological Research, 22(5):593-598.
Zhang SC, Yue BS, Zou FD. 2007. Isolation and characterization of microsatellite DNA markers from forest musk deer (Moschus berezovskii)[J]. Zoological Research, 690(24):6227-6232.
Zhao SS, Xuan C, Fang SG, et al. 2008. Development and characterization of 15 novel microsatellite markers from forest musk deer (Moschus berezovskii)[J]. Conservation Genetics, 9(3):723-725.
读者评论

      读者ID: 密码:   
我要评论:
国内统一连续出版物号:51-1193/Q |国际标准出版物号:1000-7083
主管单位:四川省科学技术协会  主办单位:四川省动物学会/成都大熊猫繁育研究基金会/四川省野生动植物保护协会/四川大学
开户银行:中国工商银行四川分行营业部东大支行(工行成都东大支行营业室)  帐户名:四川省动物学会  帐号:4402 2980 0900 0012 596
版权所有©2018四川动物》编辑部 蜀ICP备08107403号-3
您是本站第6295436名访问者

川公网安备 51010702000173号