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基于转录组测序的大熊猫多态性微卫星标记筛选
Development of Polymorphic Microsatellite Markers for Ailuropoda melanoleuca Based on RNA-Sequencing
涂洪梅, 周闯, 王冠楠, 成美玲, 岳碧松, 孟杨*
点击:372次 下载:33次
DOI:10.11984/j.issn.1000-7083.20190276
作者单位:四川大学生命科学学院, 生物资源与生态环境教育部重点实验室, 成都 610065
中文关键字:大熊猫;基因组;转录组;多态性;微卫星标记
英文关键字:Ailuropoda melanoleuca; genome; transcriptome; polymorphic; microsatellite
中文摘要:结合已公布的大熊猫Ailuropoda melanoleuca基因组和本实验室所测6只大熊猫的转录组数据,筛选多态性微卫星位点并分析其组成及特征。结果显示:共获得326个多态性微卫星位点,其中二碱基多态性微卫星最多,共228个,占69.93%;三、四、五、六碱基所占比例分别为9.51%、14.11%、5.21%、1.22%。根据分析结果中缺失率与标准差2项指标以及位点序列长度,选取20个多态性二碱基微卫星位点,用于25只大熊猫个体血液DNA进行PCR验证并做后续分析。结果表明:不同位点的等位基因数为2~8,平均等位基因数为3.70,观测杂合度、期望杂合度分别为0~1.000、0.280~0.784,平均值分别为0.472和0.532。在Bonferroni校正后,证实4个位点显著偏离哈迪-温伯格平衡,所有位点未观察到显著连锁不平衡(P>0.01)。20个位点多态信息含量(PIC)在0.246~0.734,其中具有高度多态性的位点9个(PIC>0.50),11个位点呈中度多态性(0.25 < PIC < 0.50)。本研究筛选的微卫星位点有助于评估大熊猫的遗传多样性和种群结构,并制定有效的保护和管理策略。该方法也可为后续开发更多优良微卫星位点用于大熊猫种群遗传学研究提供资源。
英文摘要:Based on the published genomes of giant pandas (Ailuropoda melanoleuca), transcriptome of 6 giant pandas were sequenced in this study to screen the polymorphic microsatellite loci and analyze their composition and characteristics. The results showed that a total of 326 polymorphic microsatellite loci were obtained, of which the dinucleotide polymorphism microsatellites accounted for a maximum of 69.93% (228 in total). The proportions of tri-, tetra-, penta-, and hexanucleotide microsatellite loci were 9.51%, 14.11%, 5.21%, and 1.22%, respectively. According to the 2 indicators, deletion rate and standard deviation, and the length of the sequence, 20 dinucleotide microsatellite loci were selected and verified in 25 giant panda individuals. Further analyses showed that the number of alleles at different loci ranged from 2 to 8, with an average value of 3.70. The observed heterozygosity and the expected heterozygosity ranged from 0 to 1.000 and 0.280 to 0.784 with the average values 0.472 and 0.532, respectively. After Bonferroni correction, it was confirmed that the 4 loci significantly deviated from the Hardy-Weinberg Equilibrium, and no significant linkage disequilibrium was observed at all loci (P>0.01). The polymorphic information content (PIC) of 20 loci ranged from 0.246 to 0.734, with 9 highly polymorphic loci (PIC>0.50), and 11 loci were moderately polymorphic (0.25 < PIC < 0.50). The microsatellite loci screened in this study can help to assess the genetic diversity and population structure of giant pandas, to develop effective conservation and management strategies, and provide resources for the subsequent development of more excellent microsatellite loci for the genetic study of giant panda population.
2020,39(1): 15-22 收稿日期:2019-08-07
分类号:Q959.8;Q347
基金项目:国家科技攻关项目(2016YFC0503200);国家自然科学基金项目(31702032)
作者简介:涂洪梅(1995-),女,硕士研究生,研究方向:分子生态学,E-mail:295047526@qq.com
*通信作者:孟杨,E-mail:mengyang@scu.edu.cn
参考文献:
李薇, 李久煊, 荆慧芳, 等. 2017. 基于高通量测序的达氏鲟微卫星标记筛选[J]. 动物学杂志, 52(3):449-457.
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.
乔麦菊, 冉江洪, 张和民, 等. 2019. 微卫星标记在大熊猫研究中的应用进展[J]. 兽类学报, 39(1):103-110.
青菁. 2016. 四川省大熊猫栖息地破碎化现状研究及廊道规划[D]. 南充:西华师范大学.
宋琪, 刘金龙, 郭宪光, 等. 2019. 基于Roche 454 GS FLX高通量测序的叶城沙蜥基因组微卫星特征分析[J]. 四川动物, 38(1):62-67.
唐小平, 贾建生, 王志臣, 等. 2015. 全国第四次大熊猫调查方案设计及主要结果分析[J]. 林业资源管理, (1):11-16.
修云芳, 李碧春, 陈玉村, 等. 2015. 应用微卫星分型进行小熊猫亲子鉴定(英文)[J]. 兽类学报, 35(1):55-64.
岳华梅, 翟晴, 宋明月, 等. 2016. 基于转录组测序的兴国红鲤微卫星标记筛选[J]. 淡水渔业, 46(1):24-28.
张正义, 邢秀梅, 胡鹏飞, 等. 2017. 微卫星标记在动物遗传多样性分析的研究进展[J]. 经济动物学报, 21(3):164-168.
Botstein D, White RL, Skolnick M, et al. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American Journal of Human Genetics, 32:314-324.
Du L, Zhang C, Liu Q, et al. 2017. Krait:an ultrafast tool for genome-wide survey of microsatellites and primer design[J]. Bioinformatics, 34(4):681-683.
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.
Haas BJ, Papanicolaou A, Yassour M, et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis[J]. Nature Protocols, 8(8):1494-1512.
He W, Lin L, Shen FJ, et al. 2008. Genetic diversities of the giant panda (Ailuropoda melanoleuca) in Wanglang and Baoxing Nature Reserve[J]. Conservation Genetics, 9:1541-1546.
Hu Y, Zhan X, Qi D, et al. 2010. Spatial genetic structure and dispersal of giant pandas on a mountain-range scale[J]. Conservation Genetics, 11(6):2145-2155.
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):61. DOI:10.1186/s12864-015-1268-z.
Jurka J, Pethiyagoda C. 1995. Simple repetitive DNA sequences from primates:compilation and analysis[J]. Journal of Molecular Evolution, 40(2):120-126.
Li WZ, Godzik A. 2006. Cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences[J]. Bioinformatics, 22(13):1658-1659.
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 (London), 282(1):39-46.
Liu HG, Yang Z, Tang HY, et al. 2017. Microsatellite development and characterization for Saurogobio dabryi Bleeker, 1871 in a Yangtze river-connected lake, China[J]. Journal of Genetics, 96:1-4.
Lu Z, Johnson WE, Menotti-Raymond M, et al. 2001. Patterns of genetic diversity in remaining giant panda populations[J]. Conservation Biology, 15(6):1596-1607.
Ma HY, Yue YS, Lu Y. 2004. Microsatellite DNA molecular marker and its application in animal breeding and genetics[J]. Journal of Animal Science & Veterinary Medicine, 23(5):16-19.
Marshall TC, Slate JB, Kruuk LE, et al. 1998. Statistical confidence for likelihood-based paternity inference in natural populations[J]. Molecular Ecology, 7(5):639-655.
Martin M. 2015. Cutadapt removes adapter sequences from high-throughput sequencing reads[J/OL]. EMBnet.jour-nal, 17(1):10-12[2019-05-05]. https://journal.embnet.org/index.php/embnetjournal/article/view/200/479. DOI:10.14806/ej.17.1.200.
Nagy S. 2012. PICcalc:an online program to calculate polymorphic information content for molecular genetic studies[J]. Biochemical Genetics, 50(9-10):670-672.
Qi WH, Jiang XM, Du LM, et al. 2015. Genome-wide survey and analysis of microsatellite sequences in bovid species[J/OL]. PLoS ONE, 10:e0133667[2019-05-05]. https://doi.org/10.1371/journal.pone.0133667.
Raymond M, Rousset F. 1995. GENEPOP (version 1.2):population genetics software for exact tests and ecumenicism[J]. Heredity, 86(3):248-249.
Ritchie H, Jamieson AJ, Piertney SB. 2016. Isolation and characterisation of microsatellite DNA markers in the deep-sea amphipod Paralicella tenuipes by Illumina Miseq sequencing[J]. Journal of Heredity, 107(4):367-371.
Selkoe KA, Toonen RJ. 2006. Microsatellites for ecologists:a practical guide to using and evaluating microsatellite markers[J]. Ecology Letters, 9(5):615-629.
Senanan W, Kapuscunski AR, Na-Nakorn U, et al. 2004. Genetic impacts of hybrid catfish faming (Clarias macrocephalus×C. gariepinus) on native catfish populations in central Thailand[J]. Aquaculture, 235(1-4):167-184.
Shen FJ, Watts P, He ZZ, et al. 2005. Enrichment of giant panda microsatellite markers using dynal magnet beads[J]. Acta Genetica Sinica, 32(5):457-462.
Shete S, Tiwari H, Elston RC. 2000. On estimating the heterozygosity and polymorphic information content value[J]. Theoretical Population Biology, 57(3):265-271.
Tian CX, Liang XF, Yang M, et al. 2014. New microsatellite loci for the mandarin fish Siniperca chuatsi and their application in population genetic analysis[J]. Genetics and Molecular Research, 13(1):546-558.
Wang D, Hu Y, Ma T, et al. 2016. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China[J]. Integrative Zoology, 11(1):16-24.
Wei F, Hu Y, Zhu L, et al. 2012. Black and white and read all over:the past, present and future of giant panda genetics[J]. Molecular Ecology, 21(23):5660-5674.
Wu H, Zhan XJ, Zhang ZJ, et al. 2008. Thirty-three microsatellite loci for noninvasive genetic studies of the giant panda (Ailuropoda melanoleuca)[J]. Conservation Genetics, 10(3):649-652.
Xia EH, Yao QY, Zhang HB, et al. 2016. CandiSSR:an efficient pipeline used for identifying candidate polymorphic SSRs based on multiple assembled sequences[J/OL]. Frontiers in Plant Science, 6:1171[2019-05-05]. https://doi.org/10.3389/fpls.2015.01171.
Xiao TQ, Lu CY, Xu YL, et al. 2015. Screening of SSR markers as sociated with scale cover pattern and mapped to a genetic linkage map of common carp (Cyprinus carpio L.)[J]. Journal of Applied Genetics, 56(2):261-269.
Xu Y, Hu Z, Wang C, et al. 2016. Characterization of perfect microsatellite based on genome-wide and chromosome level in rhesus monkey (Macaca mulatta)[J]. Gene, 592:269-275.
Zheng XF, Pan C, Diao Y, et al. 2013. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)[J/OL]. BMC Genomics, 14(1):490[2019-05-05]. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-490.
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