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Article|01 Jun 2021|OPEN
Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants
Xiaoming Song1,2,4, Qihang Yang1, Yun Bai1, Ke Gong1, Tong Wu1, Tong Yu1, Qiaoying Pei1, Weike Duan3, Zhinan Huang3, Zhiyuan Wang1, Zhuo Liu1, Xi Kang1, Wei Zhao1 & Xiao Ma1,
1School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
2School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, 610054 Chengdu, China
3College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, 223003 Huai’an, China
4Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

Horticulture Research 8,
Article number: 122 (2021)
doi: 10.1038/hortres.2021.122
Views: 204

Received: 18 Sep 2020
Revised: 10 Feb 2021
Accepted: 14 Mar 2021
Published online: 01 Jun 2021

Abstract

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.