ChloroMitoSSRDB: Open Source Repository of Perfect and Imperfect Repeats in Organelle Genomes for Evolutionary Genomics

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2013 Jan 4

PMID 23284085

Citations 14

Authors

Gaurav Sablok

Suresh B Mudunuri

Sujan Patnana

Martina Popova

Mario A Fares

Nicola La Porta

Affiliations

Soon will be listed here.

Abstract

Microsatellites or simple sequence repeats (SSRs) are repetitive stretches of nucleotides (A, T, G, C) that are distributed either as single base pair stretches or as a combination of two- to six-nucleotides units that are non-randomly distributed within coding and in non-coding regions of the genome. ChloroMitoSSRDB is a complete curated web-oriented relational database of perfect and imperfect repeats in organelle genomes. The present version of the database contains perfect and imperfect SSRs of 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes). We detected a total of 5838 chloroplast perfect SSRs, 37 297 chloroplast imperfect SSRs, 5898 mitochondrial perfect SSRs and 50 355 mitochondrial imperfect SSRs across these genomes. The repeats have been further hyperlinked to the annotated gene regions (coding or non-coding) and a link to the corresponding gene record in National Center for Biotechnology Information(www.ncbi.nlm.nih.gov/) to identify and understand the positional relationship of the repetitive tracts. ChloroMitoSSRDB is connected to a user-friendly web interface that provides useful information associated with the location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, etc. ChloroMitoSSRDB will serve as a repository for developing functional markers for molecular phylogenetics, estimating molecular variation across species. Database URL: ChloroMitoSSRDB can be accessed as an open source repository at www.mcr.org.in/chloromitossrdb.

Citing Articles

pSATdb 2.0: a database of organellar common, polymorphic, and unique microsatellites.

Kumar S, Shanker A, Gupta D Funct Integr Genomics. 2024; 24(6):213.

PMID: 39546046 DOI: 10.1007/s10142-024-01498-6.

The Complete Chloroplast Genomes of (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis.

Wu Y, Zeng M, Wang H, Lan S, Liu Z, Zhang S Int J Mol Sci. 2024; 25(5).

PMID: 38473912 PMC: 10932260. DOI: 10.3390/ijms25052665.

Chloroplast Genome Evolution and Species Identification of (Styracaceae).

Song Y, Zhao W, Xu J, Li M, Zhang Y Biomed Res Int. 2022; 2022:5364094.

PMID: 35252450 PMC: 8893999. DOI: 10.1155/2022/5364094.

pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites.

Kumar S, Singh A, Shanker A Life Sci Alliance. 2022; 5(6).

PMID: 35181599 PMC: 8860089. DOI: 10.26508/lsa.202101307.

Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species.

Sun J, Wang Y, Liu Y, Xu C, Yuan Q, Guo L Sci Rep. 2020; 10(1):11466.

PMID: 32651417 PMC: 7351712. DOI: 10.1038/s41598-020-67943-1.

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