ArticleDatabase : the journal of biological databases and curation2015
ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection.
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 32 citations in OpenAlex.
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- Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale.Scientific reports · 2023Article
- Plant mitochondrial introns as genetic markers - conservation and variation.Frontiers in plant science · 2023Article
- Towards comprehensive integration and curation of chloroplast genomes.Plant biotechnology journal · 2022Article
- Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans.Scientific reports · 2022Article
- Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.Scientific reports · 2020Article
- Repetitive DNA profile of the amphibian mitogenome.BMC bioinformatics · 2020Article
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- ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.BMC genomics · 2019Article
- Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.).Scientific reports · 2019Article
- Complete plastome sequences fromApplications in plant sciences · 2018Article
- The complete chloroplast genome ofPeerJ · 2018Article
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- A conventional PCR for differentiating common taeniid species of dogs based on in silico microsatellite analysis.Revista do Instituto de Medicina Tropical de Sao Paulo · 2017Article
- The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae).Applications in plant sciences · 2016Article
- PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers.Frontiers in plant science · 2016Article
- Towards understanding the evolution and functional diversification of DNA-containing plant organelles.F1000Research · 2016Review
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9 authors at 5 institutions in 4 countries.
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Abstract
Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics.Database URL: http://www.mcr.org.in/chloromitossrdb.
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