Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.

Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and...

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Autores principales:	Humira Sonah, Rupesh K Deshmukh, Anshul Sharma, Vinay P Singh, Deepak K Gupta, Raju N Gacche, Jai C Rana, Nagendra K Singh, Tilak R Sharma
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d9c2b2db63f14d9f9ff002f74f998cb4
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spelling	oai:doaj.org-article:d9c2b2db63f14d9f9ff002f74f998cb42021-11-18T06:51:39ZGenome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.1932-620310.1371/journal.pone.0021298https://doaj.org/article/d9c2b2db63f14d9f9ff002f74f998cb42011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21713003/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database 'BraMi' (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot-dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).Humira SonahRupesh K DeshmukhAnshul SharmaVinay P SinghDeepak K GuptaRaju N GaccheJai C RanaNagendra K SinghTilak R SharmaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 6, p e21298 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Humira Sonah Rupesh K Deshmukh Anshul Sharma Vinay P Singh Deepak K Gupta Raju N Gacche Jai C Rana Nagendra K Singh Tilak R Sharma Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.
description	Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database 'BraMi' (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot-dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).
format	article
author	Humira Sonah Rupesh K Deshmukh Anshul Sharma Vinay P Singh Deepak K Gupta Raju N Gacche Jai C Rana Nagendra K Singh Tilak R Sharma
author_facet	Humira Sonah Rupesh K Deshmukh Anshul Sharma Vinay P Singh Deepak K Gupta Raju N Gacche Jai C Rana Nagendra K Singh Tilak R Sharma
author_sort	Humira Sonah
title	Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.
title_short	Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.
title_full	Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.
title_fullStr	Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.
title_full_unstemmed	Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.
title_sort	genome-wide distribution and organization of microsatellites in plants: an insight into marker development in brachypodium.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/d9c2b2db63f14d9f9ff002f74f998cb4
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Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.

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