CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences

doi:10.3389/fpls.2015.01771

	CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences
	Xia, En-Hua; Yao, Qiu-Yang; Zhang, Hai-Bin; Jiang, Jian-Jun; Zhang, Li-Ping; Gao, Li-Zhi
	2016-01-07
发表期刊	FRONTIERS IN PLANT SCIENCE
卷号	6
摘要	Simple sequence repeats (SSRs), also known as microsatellites, are ubiquitous short tandem duplications commonly found in genomes and/or transcriptomes of diverse organisms. They represent one of the most powerful molecular markers for genetic analysis and breeding programs because of their high mutation rate and neutral evolution. However, traditionally experimental screening of the SSR polymorphic status and their subsequent applicability to genetic studies are extremely labor-intensive and time-consuming. Thankfully, the recently decreased costs of next generation sequencing and increasing availability of large genome and/or transcriptome sequences have provided an excellent opportunity and sources for large-scale mining this type of molecular markers. However, current tools are limited. Thus we here developed a new pipeline, CandiSSR, to identify candidate polymorphic SSRs (PolySSRs) based on the multiple assembled sequences. The pipeline allows users to identify putative PolySSRs not only from the transcriptome datasets but also from multiple assembled genome sequences. In addition, two confidence metrics including standard deviation and missing rate of the SSR repetitions are provided to systematically assess the feasibility of the detected PolySSRs for subsequent application to genetic characterization. Meanwhile, primer pairs for each identified PolySSR are also automatically designed and further evaluated by the global sequence similarities of the primer binding region, ensuring the successful rate of the marker development. Screening rice genomes with CandiSSR and subsequent experimental validation showed an accuracy rate of over 90%. Besides, the application of CandiSSR has successfully identified a large number of PolySSRs in the Arabidopsis genomes and Camellia transcriptomes. CandiSSR and the PolySSR marker sources are publicly available at: http://www.plantkingdomgdb.com/CandiSSR/index.html.
关键词	Microsatellites Transferability Polymorphic Ssr Candissr Multiple Assembled Genomes Multiple Assembled Transcriptomes
DOI	10.3389/fpls.2015.01771
收录类别	SCI
语种	英语
WOS记录号	WOS:000367684300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/25441
专题	中国西南野生生物种质资源库
推荐引用方式 GB/T 7714	Xia, En-Hua,Yao, Qiu-Yang,Zhang, Hai-Bin,et al. CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences[J]. FRONTIERS IN PLANT SCIENCE,2016,6.
APA	Xia, En-Hua,Yao, Qiu-Yang,Zhang, Hai-Bin,Jiang, Jian-Jun,Zhang, Li-Ping,&Gao, Li-Zhi.(2016).CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences.FRONTIERS IN PLANT SCIENCE,6.
MLA	Xia, En-Hua,et al."CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences".FRONTIERS IN PLANT SCIENCE 6(2016).

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
fpls-06-01171.pdf（3466KB）	期刊论文	作者接受稿	开放获取	CC BY-NC-SA	浏览下载