ArticleScientific reports2016
A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 88 citations in OpenAlex.
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- Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species.Scientific reports · 2023Article
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- Fine Mapping and Gene Analysis ofInternational journal of molecular sciences · 2022Article
- Genome-Wide Survey and Development of the First Microsatellite Markers Database (International journal of molecular sciences · 2022Article
- LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement.International journal of molecular sciences · 2021Article
- Fine mapping and candidate gene analysis of the up locus determining fruit orientation in pepper (Capsicum spp.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.).Scientific reports · 2021Article
- Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Frontiers in plant science · 2021Article
- Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Frontiers in plant science · 2021Article
- A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts inInternational journal of genomics · 2021Article
- Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae).Journal of insect science (Online) · 2020Article
- The Complete Chloroplast Genome ofInternational journal of genomics · 2020Article
- Microsatellite Borders and Micro-sequence Conservation in Juglans.Scientific reports · 2019Article
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Authors and funding
11 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.
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