Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
Main Author: | |
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Publication Date: | 2012 |
Other Authors: | , , |
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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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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1808128384477167616 |