title: ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection.
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.
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia, Environmental Biotechnology Platform, Research and Innovation Center, Fondazione Edmund Mach (FEM), IASMA Via Mach 1., 38010 San Michele all'Adige (TN), Italy, sablokg@gmail.com.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
authors.affiliation: Department of Computer Science and Engineering, S.R.K.R Engineering College, Chinna Amiram, Bhimavaram 534204, Andhra Pradesh, India.
authors.forename: G V
authors.initials: GV
authors.lastname: Padma Raju
authors.affiliation: Technology Centre, S.R.K.R. Engineering College, Chinna Amiram, Bhimavaram 534204, Andhra Pradesh, India.
authors.forename: Suresh B
authors.initials: SB
authors.lastname: Mudunuri
authors.affiliation: National Bureau of Agriculturally Important Microorganisms (NBAIM) (Indian Council of Agricultural Research), Maunath Bhanjan 275101, Uttar Pradesh, India and.
authors.forename: Ratna
authors.initials: R
authors.lastname: Prabha
authors.affiliation: National Bureau of Agriculturally Important Microorganisms (NBAIM) (Indian Council of Agricultural Research), Maunath Bhanjan 275101, Uttar Pradesh, India and.
authors.forename: Dhananjaya P
authors.initials: DP
authors.lastname: Singh
authors.affiliation: Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
authors.forename: Vesselin
authors.initials: V
authors.lastname: Baev
authors.affiliation: Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
authors.forename: Galina
authors.initials: G
authors.lastname: Yahubyan
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Ralph
authors.affiliation: Environmental Biotechnology Platform, Research and Innovation Center, Fondazione Edmund Mach (FEM), IASMA Via Mach 1., 38010 San Michele all'Adige (TN), Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: La Porta
mesh_terms: D030541:Databases, Genetic; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D020407:Internet; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010944:Plants / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods