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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
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Your Position :Home->Past Journals Catalog->2017 Vol.36 No.4

Distribution Regularity of Microsatellites in Moschus berezovskii Genome
Author of the article:LU Ting1#, WANG Chen1#, DU Chao1, LIU Shu2, SHEN Yongmei2, ZHANG Xiuyue1, YUE Bisong1*
Author's Workplace:1. Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China;
2. Sichuan Medicinal Animal Engineering Technology Research Center, Chengdu 610081, China
Key Words:Moschus berezovskii; genome; microsatellite; distribution regularities
Abstract: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
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.
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