Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major
Xiaoming Song1,2,3, Qihang Yang4, Yun Bai4
1School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China. songxm@ncst.edu.cn.
Horticulture Research
|June 1, 2021
Summary
This study identified over 249,000 simple sequence repeats (SSRs) in 112 plant species, creating a valuable database for genetic research. The findings reveal differences in SSR distribution between lower and higher plants, aiding evolutionary studies.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- Simple sequence repeats (SSRs) are crucial genetic markers found across many species.
- Understanding SSR distribution and function is vital for plant genomics and evolutionary studies.
Purpose of the Study:
- To identify and comprehensively analyze SSRs in a large collection of plant genes.
- To construct a publicly accessible plant SSR database (PSSRD) with user-friendly tools.
- To investigate the evolutionary implications of SSR distribution, particularly between lower and higher plants.
Main Methods:
- Identification and analysis of 249,822 SSRs from 3,951,919 genes across 112 plant species.
- Construction of the Plant SSR Database (PSSRD) with interactive visualization and data download capabilities.
- Development of Web SSR Finder and Batch SSR Finder tools for SSR identification.
Main Results:
- A significant difference in SSR abundance was observed between lower and higher plants, suggesting adaptation to early environments.
- Enriched functional terms and higher prevalence of Guanylate_cyc in lower plant genes were identified.
- The PSSRD provides comprehensive SSR data, including sequences, primers, and annotations, with user-friendly access and analysis tools.
- Applications using Myb gene families and flowering genes demonstrated the utility of the PSSRD for genomic studies, highlighting the role of genome duplication in gene family expansion.
Conclusions:
- The PSSRD is a valuable resource for plant genomics, facilitating comparative and functional studies.
- SSR distribution patterns offer insights into plant adaptation and evolution.
- The developed tools enhance the accessibility and utility of SSR data for researchers worldwide.
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