Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.

One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species...

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Autores principales:	Ana Rodríguez-Prieto, Javier Igea, Jose Castresana
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/379f3c1b1fc7460496942721cfb73e45
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spelling	oai:doaj.org-article:379f3c1b1fc7460496942721cfb73e452021-11-18T08:20:25ZDevelopment of rapidly evolving intron markers to estimate multilocus species trees of rodents.1932-620310.1371/journal.pone.0096032https://doaj.org/article/379f3c1b1fc7460496942721cfb73e452014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24804779/?tool=EBIhttps://doaj.org/toc/1932-6203One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity, but so far no systematic study has been carried out to detect suitable informative markers for this group. Here, we used a bioinformatic pipeline to extract intron sequences from rodent genomes available in databases and applied a series of filters that allowed the identification of 208 introns that adequately fulfilled several criteria for these studies. The main required characteristics of the introns were that they had the maximum possible mutation rates, that they were part of single-copy genes, that they had an appropriate sequence length for amplification, and that they were flanked by exons with suitable regions for primer design. In addition, in order to determine the validity of this approach, we chose ten of these introns for primer design and tested them in a panel of eleven rodent species belonging to different representative families. We show that all these introns can be amplified in the majority of species and that, overall, 79% of the amplifications worked with minimum optimization of the annealing temperature. In addition, we confirmed for a pair of sister species the relatively high level of sequence divergence of these introns. Therefore, we provide here a set of adequate intron markers that can be applied to different species of Rodentia for their use in studies that require significant sequence variability.Ana Rodríguez-PrietoJavier IgeaJose CastresanaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 5, p e96032 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ana Rodríguez-Prieto Javier Igea Jose Castresana Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
description	One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity, but so far no systematic study has been carried out to detect suitable informative markers for this group. Here, we used a bioinformatic pipeline to extract intron sequences from rodent genomes available in databases and applied a series of filters that allowed the identification of 208 introns that adequately fulfilled several criteria for these studies. The main required characteristics of the introns were that they had the maximum possible mutation rates, that they were part of single-copy genes, that they had an appropriate sequence length for amplification, and that they were flanked by exons with suitable regions for primer design. In addition, in order to determine the validity of this approach, we chose ten of these introns for primer design and tested them in a panel of eleven rodent species belonging to different representative families. We show that all these introns can be amplified in the majority of species and that, overall, 79% of the amplifications worked with minimum optimization of the annealing temperature. In addition, we confirmed for a pair of sister species the relatively high level of sequence divergence of these introns. Therefore, we provide here a set of adequate intron markers that can be applied to different species of Rodentia for their use in studies that require significant sequence variability.
format	article
author	Ana Rodríguez-Prieto Javier Igea Jose Castresana
author_facet	Ana Rodríguez-Prieto Javier Igea Jose Castresana
author_sort	Ana Rodríguez-Prieto
title	Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
title_short	Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
title_full	Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
title_fullStr	Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
title_full_unstemmed	Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
title_sort	development of rapidly evolving intron markers to estimate multilocus species trees of rodents.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/379f3c1b1fc7460496942721cfb73e45
work_keys_str_mv	AT anarodriguezprieto developmentofrapidlyevolvingintronmarkerstoestimatemultilocusspeciestreesofrodents AT javierigea developmentofrapidlyevolvingintronmarkerstoestimatemultilocusspeciestreesofrodents AT josecastresana developmentofrapidlyevolvingintronmarkerstoestimatemultilocusspeciestreesofrodents
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Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.

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