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Genome-wide protein phylogenies for four African cichlid species

BACKGROUND: The thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequ...

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Autores principales: Ramakrishnan Varadarajan, Ajay, Mopuri, Rohini, Streelman, J. Todd, McGrath, Patrick T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784529/
https://www.ncbi.nlm.nih.gov/pubmed/29368592
http://dx.doi.org/10.1186/s12862-017-1072-2
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author Ramakrishnan Varadarajan, Ajay
Mopuri, Rohini
Streelman, J. Todd
McGrath, Patrick T.
author_facet Ramakrishnan Varadarajan, Ajay
Mopuri, Rohini
Streelman, J. Todd
McGrath, Patrick T.
author_sort Ramakrishnan Varadarajan, Ajay
collection PubMed
description BACKGROUND: The thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species. RESULTS: We used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented. CONCLUSION: These phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-017-1072-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-57845292018-02-07 Genome-wide protein phylogenies for four African cichlid species Ramakrishnan Varadarajan, Ajay Mopuri, Rohini Streelman, J. Todd McGrath, Patrick T. BMC Evol Biol Database BACKGROUND: The thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species. RESULTS: We used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented. CONCLUSION: These phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-017-1072-2) contains supplementary material, which is available to authorized users. BioMed Central 2018-01-08 /pmc/articles/PMC5784529/ /pubmed/29368592 http://dx.doi.org/10.1186/s12862-017-1072-2 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Database
Ramakrishnan Varadarajan, Ajay
Mopuri, Rohini
Streelman, J. Todd
McGrath, Patrick T.
Genome-wide protein phylogenies for four African cichlid species
title Genome-wide protein phylogenies for four African cichlid species
title_full Genome-wide protein phylogenies for four African cichlid species
title_fullStr Genome-wide protein phylogenies for four African cichlid species
title_full_unstemmed Genome-wide protein phylogenies for four African cichlid species
title_short Genome-wide protein phylogenies for four African cichlid species
title_sort genome-wide protein phylogenies for four african cichlid species
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784529/
https://www.ncbi.nlm.nih.gov/pubmed/29368592
http://dx.doi.org/10.1186/s12862-017-1072-2
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