Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish

Bibliographic Details
Main Author: Mazzuchelli, Juliana [UNESP]
Publication Date: 2012
Other Authors: Kocher, Thomas David, Yang, Fengtang, Martins, Cesar [UNESP]
Format: Article
Language: eng
Source: Repositório Institucional da UNESP
Download full: http://dx.doi.org/10.1186/1471-2164-13-463
http://hdl.handle.net/11449/18742
Summary: Background: The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence in situ hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an Oreochromis niloticus library covering the linkage groups (LG) 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of O. niloticus and comparatively analyzed against the genome of other fish species and vertebrates.Results: The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative in silico analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates.Conclusions: Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.
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spelling Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fishCichlidaeGenome evolutionMolecular cytogeneticsChromosomeLinkage groupsBACsBackground: The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence in situ hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an Oreochromis niloticus library covering the linkage groups (LG) 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of O. niloticus and comparatively analyzed against the genome of other fish species and vertebrates.Results: The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative in silico analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates.Conclusions: Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Wellcome TrustUNESP São Paulo State Univ, Biosci Inst, Dept Morphol, BR-18618970 Botucatu, SP, BrazilUniv Maryland, Dept Biol, College Pk, MD 20742 USAWellcome Trust Sanger Inst, Cambridge CB10 1SA, EnglandUNESP São Paulo State Univ, Biosci Inst, Dept Morphol, BR-18618970 Botucatu, SP, BrazilWellcome Trust: WT098051Biomed Central Ltd.Universidade Estadual Paulista (Unesp)University of MarylandWellcome Trust Sanger InstMazzuchelli, Juliana [UNESP]Kocher, Thomas DavidYang, FengtangMartins, Cesar [UNESP]2014-05-20T13:52:28Z2014-05-20T13:52:28Z2012-09-09info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article14application/pdfhttp://dx.doi.org/10.1186/1471-2164-13-463Bmc Genomics. London: Biomed Central Ltd., v. 13, p. 14, 2012.1471-2164http://hdl.handle.net/11449/1874210.1186/1471-2164-13-463WOS:000309413900001WOS000309413900001.pdf88588006994253520000-0003-3534-974XWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomics3.7302,110info:eu-repo/semantics/openAccess2023-10-11T06:04:13Zoai:repositorio.unesp.br:11449/18742Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:35:45.327164Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
title Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
spellingShingle Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
Mazzuchelli, Juliana [UNESP]
Cichlidae
Genome evolution
Molecular cytogenetics
Chromosome
Linkage groups
BACs
title_short Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
title_full Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
title_fullStr Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
title_full_unstemmed Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
title_sort Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
author Mazzuchelli, Juliana [UNESP]
author_facet Mazzuchelli, Juliana [UNESP]
Kocher, Thomas David
Yang, Fengtang
Martins, Cesar [UNESP]
author_role author
author2 Kocher, Thomas David
Yang, Fengtang
Martins, Cesar [UNESP]
author2_role author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
University of Maryland
Wellcome Trust Sanger Inst
dc.contributor.author.fl_str_mv Mazzuchelli, Juliana [UNESP]
Kocher, Thomas David
Yang, Fengtang
Martins, Cesar [UNESP]
dc.subject.por.fl_str_mv Cichlidae
Genome evolution
Molecular cytogenetics
Chromosome
Linkage groups
BACs
topic Cichlidae
Genome evolution
Molecular cytogenetics
Chromosome
Linkage groups
BACs
description Background: The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence in situ hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an Oreochromis niloticus library covering the linkage groups (LG) 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of O. niloticus and comparatively analyzed against the genome of other fish species and vertebrates.Results: The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative in silico analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates.Conclusions: Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.
publishDate 2012
dc.date.none.fl_str_mv 2012-09-09
2014-05-20T13:52:28Z
2014-05-20T13:52:28Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1186/1471-2164-13-463
Bmc Genomics. London: Biomed Central Ltd., v. 13, p. 14, 2012.
1471-2164
http://hdl.handle.net/11449/18742
10.1186/1471-2164-13-463
WOS:000309413900001
WOS000309413900001.pdf
8858800699425352
0000-0003-3534-974X
url http://dx.doi.org/10.1186/1471-2164-13-463
http://hdl.handle.net/11449/18742
identifier_str_mv Bmc Genomics. London: Biomed Central Ltd., v. 13, p. 14, 2012.
1471-2164
10.1186/1471-2164-13-463
WOS:000309413900001
WOS000309413900001.pdf
8858800699425352
0000-0003-3534-974X
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv BMC Genomics
3.730
2,110
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 14
application/pdf
dc.publisher.none.fl_str_mv Biomed Central Ltd.
publisher.none.fl_str_mv Biomed Central Ltd.
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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