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IDSSR: An Efficient Pipeline for Identifying Polymorphic Microsatellites from a Single Genome Sequence.

Xuan-Min Guang1, Jin-Quan Xia1, Jian-Qing Lin1

  • 1MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.

International Journal of Molecular Sciences
|July 19, 2019
PubMed
Summary

A new method, insertion/deletion SSR (IDSSR), efficiently identifies polymorphic simple sequence repeats (SSRs) using genome sequences and paired-end reads. This reduces time and cost for genetic marker discovery in various species.

Keywords:
IDSSRINDELefficienthigh qualitypolymorphic SSRs

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Simple sequence repeats (SSRs), also known as microsatellites, are valuable molecular markers.
  • Traditional SSR identification and validation are time-consuming and expensive.

Purpose of the Study:

  • To develop an efficient and cost-effective method for identifying polymorphic SSRs.
  • To integrate SSR identification with nucleotide insertions/deletions (INDELs) for enhanced marker discovery.

Main Methods:

  • Developed the Insertion/Deletion SSR (IDSSR) strategy.
  • Utilized single genome sequences and paired-end reads for analysis.
  • Identified INDEL indexes, repeat numbers, motifs, chromosome locations, and primer sequences.

Main Results:

  • The IDSSR method successfully identified polymorphic SSRs.
  • Experimental validation in giant pandas confirmed high reliability and stability.
  • The pipeline provides comprehensive data for experimental validation.

Conclusions:

  • The IDSSR pipeline offers an efficient approach for discovering high-quality genetic markers.
  • This method saves labor and reduces costs associated with traditional marker screening.
  • IDSSR is a valuable tool for researchers in molecular ecology, conservation biology, and breeding.