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

Frontiers in Plant Science
En-Hua XiaLi-Zhi Gao

Abstract

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 feasibil...Continue Reading

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Citations

Mar 12, 2020·Database : the Journal of Biological Databases and Curation·Himanshu DubeyTapan Kumar Mondal
Oct 27, 2018·Nucleic Acids Research·Morad M Mokhtar, Mohamed A M Atia
Mar 27, 2019·Plant Biotechnology Journal·En-Hua XiaXiao-Chun Wan
Jul 19, 2019·International Journal of Molecular Sciences·Xuan-Min GuangSheng-Guo Fang

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Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

SSRPrimer
Linux
MySQL
CandiSSR
CheckSSR
Primer3
SSR Primer
Sputnik
Perl script
BASH

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