ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants

Abstract

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants.Database URL: www.compubio.in/chlorossrdb/

In Silico Comparative Analysis of Simple Sequence Repeats in Chloroplast Genomes of Genus Nymphaea

“…These repeats found in coding and non-coding regions of both prokaryotic and eukaryotic genomes. Moreover, SSRs are also present in organellar genomes including chloroplast and amitochondria (Kapil et al, 2014;Kumar et al, 2014). SSRs have a higher mutation rate than other areas of genomes (Brinkmann et al, 1998) leading to high genetic diversity.…”

“…Computational approaches have become a relatively less time consuming and inexpensive to develop SSRs. Previously, using computational approaches SSRs were mined in large amount of sequence data retrieved from National Centre for Biotechnology Information (NCBI) and online databases were developed for obtained information (Kapil et al, 2014;Kumar et al, 2014;Kabra et al, 2016). The availability of nucleotide/genome sequence of various organisms in biological databases proved to be a fast and inexpensive way for computational mining of SSRs (Shanker, 2013(Shanker, , 2014Shanker, 2016;Kumar & Shanker, 2018c).…”

ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

“…Previously developed organelle repositories such as FUGOID ( 16 ), primer respository for chloroplast genomes ( 17 ), GOBASE ( 18 ) and AT_CHLORO ( 19 ), although provides a wide array of curated information on certain aspects of organelle genomics, they lack SSRs information, which motivated the earlier establishment of ChloroMitoSSRDB ( 9 ), as an integrated open-access portal for browsing SSRs patterns from organelle genomes across several clades of organism. Following this approach, two SSRs repositories, namely MitoSatPlant ( 15 ) and ChloroSSRdb ( 20 ) have been developed specifically focusing on plant species. However, despite the development of these plant centric repositories, a unifying portal for the comparative visualization of repeats incorporating several organisms and ‘on-the-fly’ repeat mining from either the gene or genome-based organelle assemblies or the next generation sequencing (NGS) reads is still lacking.…”

Iberian Peninsula cowpea diversity: chloroplast, microsatellite and morpho-agronomic variability

“…The shared haplotype between these two forms of cultivated cowpea suggests a highly conserved nature of the chloroplast genome with a low mutation rate in the worldwide germplasm of cultivated forms of V. unguiculata subsp. unguiculata (Kapil et al, 2014;Palmer, 1985;Vaillancourt & Weeden, 1992). Nuclear SNP markers enable population structuring of cultivated cowpea that differentiates between sesquipedalis and unguiculata germplasm, regardless of the origin of the sesquipedalis material (Carvalho, Muñoz-Amatria ın, et al, 2017).…”