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

Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae

“…Chloroplast simple sequence repeats (cpSSRs) in B. excelsa were identified using the Phobos Tandem Repeat Finder version 3.3.12 (Mayer, ) by searching for uninterrupted repeats of nucleotide units of 1 to 6 bp in length, with thresholds of ≥12 mononucleotide, ≥6 dinucleotide, and ≥4 trinucleotide repeats, and ≥3 tetra‐, penta‐, and hexanucleotide repeats (Sablok et al., ). We developed primers to amplify the cpSSRs using Primer3 version 2.3.4 (Untergasser et al., ) with the default options and setting the PCR product size range between 100 and 300 bp.…”

Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss

“…SSRs are common in plant and animal genomes and could play an important role in gene functioning (Li et al, 2004). Besides the occurrence of the SSR loci in nuclear genomes, microsatellite repeats are present in plastids and MGs as well (Kumar, Kapil, & Shanker, 2014;Sablok, 2015). However, to date, it is much less known about distribution and functions of microsatellites in bryophyte genomes.…”

Peer Review #1 of "Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss (v0.1)"

“…SSRs are common in plant and animal genomes and could play an important role in gene functioning (Li et al, 2004). Besides the occurrence of the SSR loci in nuclear genomes, microsatellite repeats are present in plastids and MGs as well (Kumar, Kapil, & Shanker, 2014;Sablok, 2015). However, to date, it is much less known about distribution and functions of PeerJ reviewing PDF | (2017:08:20076:2:0:NEW 18 Jan 2018)…”