ArticleHorticulture research2021
Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants.
Article in Horticulture research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 48 citations in OpenAlex.
- PlantRG: A Comprehensive and User-Friendly Database for Plant Resistance Gene Analogs (RGAs).Plant biotechnology journal · 2026Article
- Comprehensive genomic analysis and database construction for Apiales.Journal of advanced research · 2026Article
- SSR marker development for analysis of the genetic diversity and identification of species and infraspecific ranks in the genus Phyllostachys.BMC plant biology · 2026Article
- Abiotic stress-responsive transcription factor derived-SSR markers reveal conserved regulatory genes and genetic structure in two cultivated jute species.BMC plant biology · 2026Article
- Identification and Development of Pathogen- and Pest-Specific Defense-Resistance-Associated SSR Marker Candidates Assisted by Machine Learning and Discovery of Putative QTL Hotspots inPlants (Basel, Switzerland) · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genomes ofFrontiers in plant science · 2026Article
- RNA-Seq-based transcriptomics reveals differential gene expression between two Pisum sativum subspecies and uncovers their molecular marker profiles.BMC genomics · 2025Article
- Development of Genome-Wide SSR Markers inInternational journal of molecular sciences · 2025Article
- Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb.Database : the journal of biological databases and curation · 2024Article
- Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).BMC plant biology · 2024Article
- Genome-Wide Characterization and Development of Simple Sequence Repeat Markers for Molecular Diversity Analyses in Yellowhorn (Plants (Basel, Switzerland) · 2024Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- Fine-tuning plant valuable secondary metabolite biosynthesis via small RNA manipulation: strategies and potential.Planta · 2024Review
- Genome-wide simple sequence repeat analysis and specific molecular marker development of rye.BMC genomics · 2024Article
- Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD.The plant genome · 2024Article
- Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers.Scientific reports · 2024Article
- Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants.Molecular horticulture · 2024Article
- Flowering genes identification, network analysis, and database construction for 837 plants.Horticulture research · 2024Article
- Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae.Plants (Basel, Switzerland) · 2024Article
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Corrections and comments
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
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