Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.
Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.
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DOI：
10.1186/s12864-015-1268-z
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发表时间：
2015-02-07
期刊：
影响因子：
4.4
通讯作者：
Yue BS
中科院分区：
文献类型：
--
作者：
Huang J;Li YZ;Du LM;Yang B;Shen FJ;Zhang HM;Zhang ZH;Zhang XY;Yue BS
大熊猫（Ailuropoda melanoleuca）是中国特有的极度濒危物种。微卫星作为最常用的分子标记，已被证明在极危物种的种群规模、亲子鉴定、遗传多样性等方面具有良好的应用前景。大熊猫全基因组序列的获得为对所有类型的微卫星标记进行全基因组扫描提供了机会，为大熊猫微卫星的分析和开发开辟了道路。通过对大熊猫全基因组序列的筛选，确定了大熊猫基因组中的微卫星位点，并分析了微卫星位点在大熊猫基因组不同区域的频率和分布。根据我们的搜索标准，检测到855，058个SSR的库，其中单核苷酸最丰富。SSR在所有基因组区域都有发现，并且在非编码区比编码区更丰富。共设计了160对引物，利用选定的四核苷酸微卫星序列筛选多态性微卫星。本研究通过对22只圈养大熊猫血液DNA进行基因分型，发现了51个新的多态性四核苷酸微卫星位点。最后，利用15个在粪便样品中表现出良好多态性、稳定性和重复性的标记，建立了大熊猫微卫星标记新体系。同时，利用该标准化系统建立了成都圈养大熊猫（n = 57）的基因分型数据库。作为该标记体系的应用，本研究还建立了一种通用的个体识别方法，并对该标记体系的遗传多样性进行了分析。大熊猫基因组中微卫星的丰度和多样性具有一定的特征。共检测到154，677个四核苷酸微卫星位点，其中15个位点具有多态性和稳定性。本研究中的个体鉴定方法和遗传多样性分析方法为大熊猫的进一步研究提供了充足的材料。本文的在线版本（doi：10.1186/s12864-015-1268-z）包含补充材料，可供授权用户使用。
The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda. By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What’s more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system. The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda. The online version of this article (doi:10.1186/s12864-015-1268-z) contains supplementary material, which is available to authorized users.
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影响因子：
7.7
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
通讯作者：
Pollock DD
影响因子：
10.7
作者：
Karaoglu, H;Lee, CMY;Meyer, W
通讯作者：
Meyer, W
DOI：
10.1111/j.1471-8286.2007.01826.x
发表时间：
2007-11-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
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通讯作者：
Wade, Michael J.
影响因子：
2
作者：
Kolodziej, K.;Theissinger, K.;Schulz, R.
通讯作者：
Schulz, R.
影响因子：
2.5
作者：
Labbe, Jessy;Murat, Claude;Martin, Francis
通讯作者：
Martin, Francis