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.
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1 North China University of Science and Technology, School of Life Sciences/Library, Tangshan, China (GRID:grid.440734.0) (ISNI:0000 0001 0707 0296); University of Electronic Science and Technology of China, School of Life Science and Technology and Center for Informational Biology, Chengdu, China (GRID:grid.54549.39) (ISNI:0000 0004 0369 4060); University of Nebraska-Lincoln, Food Science and Technology Department, Lincoln, USA (GRID:grid.24434.35) (ISNI:0000 0004 1937 0060)
2 North China University of Science and Technology, School of Life Sciences/Library, Tangshan, China (GRID:grid.440734.0) (ISNI:0000 0001 0707 0296)
3 Huaiyin Institute of Technology, College of Life Sciences and Food Engineering, Huai’an, China (GRID:grid.417678.b) (ISNI:0000 0004 1800 1941)