植物多样性 2017, 39(05) 294-299 DOI:   10.1016/j.pld.2017.05.008  ISSN: 2096-2703 CN: 53-1233

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MiddRAD-seq
Endangered species
Microsatellite
Next-generation sequencing
Taxus florinii
本文作者相关文章
PubMed
Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species
Hantao Qina,b, Guoqian Yangb,c, Jim Provand, Jie Liua, Lianming Gaoa
a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b University of Chinese Academy of Sciences, Beijing, 100049, China;
c Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China;
d Institute of Biological, Environmental and Rural Sciences(IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, UK
摘要: Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean=4.875), and within-population expected heterozygosity from zero to 0.789 (mean=0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
关键词 MiddRAD-seq   Endangered species   Microsatellite   Next-generation sequencing   Taxus florinii  
Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species
Hantao Qina,b, Guoqian Yangb,c, Jim Provand, Jie Liua, Lianming Gaoa
a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b University of Chinese Academy of Sciences, Beijing, 100049, China;
c Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China;
d Institute of Biological, Environmental and Rural Sciences(IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, UK
Abstract: Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean=4.875), and within-population expected heterozygosity from zero to 0.789 (mean=0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
Keywords: MiddRAD-seq   Endangered species   Microsatellite   Next-generation sequencing   Taxus florinii  
收稿日期 2017-01-19 修回日期 2017-05-27 网络版发布日期  
DOI: 10.1016/j.pld.2017.05.008
基金项目:

This research was funded by the National Natural Science Foundations of China (31370252,41571059) and the National Key Basic Research Program of China (2014CB954100).

通讯作者: Jie Liu,E-mail addresses:liujie@mail.kib.ac.cn;Lianming Gao,E-mail addresses:gaolm@mail.kib.ac.cn
作者简介:
作者Email: liujie@mail.kib.ac.cn;gaolm@mail.kib.ac.cn

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