Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades

Detalhes bibliográficos
Autor(a) principal: Vialle, Ricardo Assunção
Data de Publicação: 2018
Outros Autores: Souza, Jorge Estefano Santana de, Lopes, Katia de Paiva, Teixeira, Diego Gomes, Alves Sobrinho, Pitágoras de Azevedo, Ribeiro-dos-Santos, André M, Furtado, Carolina, Sakamoto, Tetsu, Silva, Fábio Augusto Oliveira, Oliveira, Edivaldo Herculano Correa de, Hamoy, Igor Guerreiro, Assumpção, Paulo Pimentel, Ribeiro-dos-Santos, Ândrea, Lima, João Paulo Mattos Santos, Seuánez, Héctor N, Souza, Sandro José de, Santos, Sidney
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Digital do Instituto Evandro Chagas (Patuá)
Texto Completo: https://patua.iec.gov.br/handle/iec/3515
Resumo: The Pirarucu (Arapaima gigas) is one of the world’s largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.
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spelling Vialle, Ricardo AssunçãoSouza, Jorge Estefano Santana deLopes, Katia de PaivaTeixeira, Diego GomesAlves Sobrinho, Pitágoras de AzevedoRibeiro-dos-Santos, André MFurtado, CarolinaSakamoto, TetsuSilva, Fábio Augusto OliveiraOliveira, Edivaldo Herculano Correa deHamoy, Igor GuerreiroAssumpção, Paulo PimentelRibeiro-dos-Santos, ÂndreaLima, João Paulo Mattos SantosSeuánez, Héctor NSouza, Sandro José deSantos, Sidney2018-10-22T13:40:27Z2018-10-22T13:40:27Z2018VIALLE, Ricardo Assunção et al. Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades. Genome Biology and evolution, v. 10, n. 9, p. 2366-2379, Sept. 2018.1759-6653https://patua.iec.gov.br/handle/iec/351510.1093/gbe/evy130The Pirarucu (Arapaima gigas) is one of the world’s largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.This work was supported by Rede de Pesquisa em Genômica Populacional Humana (RPGPH)—3381/2013 CAPES-BioComputacional; FADESP/PROPESP/UFPA (Universidade Federal do Pará); and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico). It was also supported by CNPq/Produtividade grant 304413/2015-1 to A.R.S. and CNPq/Produtividade grant 305258/2013-3 to S.S.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Genética Humana e Médica. Belém, PA, Brazil.Universidade Federal do Rio Grande do Norte. Bioinformatics Multidisciplinary Environment. Natal, RN, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Genética Humana e Médica. Belém, PA, Brazil.Universidade Federal do Rio Grande do Norte. Bioinformatics Multidisciplinary Environment. Natal, RN, Brazil.Universidade Federal do Rio Grande do Norte. Bioinformatics Multidisciplinary Environment. Natal, RN, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Genética Humana e Médica. Belém, PA, Brazil / Universidade Federal do Rio Grande do Norte. Departmento de Genética. Natal, RN, Brazil.Instituto Nacional de Câncer. Programa de Genética. Rio de Janeiro, RJ, Brazil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Laboratório de Cultura de Tecidos e Citogenética. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Laboratório de Cultura de Tecidos e Citogenética. Ananindeua, PA, Brasil.Universidade Federal Rural da Amazônia. Laboratório de Genética Aplicada. Belém, PA, Brazil.Universidade Federal do Pará. Núcleo de Pesquisas em Oncologia. Belém, PA, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Genética Humana e Médica. Belém, PA, Brazil / Universidade Federal do Pará. Núcleo de Pesquisas em Oncologia. Belém, PA, Brazil.Universidade Federal do Rio Grande do Norte. Bioinformatics Multidisciplinary Environment. Natal, RN, Brazil / Universidade Federal do Rio Grande do Norte. Departamento de Bioquímica. Natal, RN, Brazil.Instituto Nacional de Câncer. Programa de Genética. Rio de Janeiro, RJ, Brazil / Universidade Federal do Rio de Janeiro. Departamento de Genética. Rio de Janeiro, RJ, Brazil.Universidade Federal do Rio Grande do Norte. Bioinformatics Multidisciplinary Environment. Natal, RN, Brazil / Universidade Federal do Rio Grande do Norte. Instituto do Cérebro. Natal, RN, Brazil.Universidade Federal do Pará. Instituto de Ciências Biológicas. Laboratório de Genética Humana e Médica. Belém, PA, Brazil / Universidade Federal do Pará. Núcleo de Pesquisas em Oncologia. Belém, PA, Brazil.engOxford University PressWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost cladesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePeixes / anatomia & histologiaPeixes / genéticaGenoma / fisiologiaMapeamento Cromossômico / métodosBacia do Rio Amazonas (BR)PirarucuArapaima gigasinfo:eu-repo/semantics/openAccessreponame:Repositório Digital do Instituto Evandro Chagas (Patuá)instname:Instituto Evandro Chagas (IEC)instacron:IECORIGINALWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades.pdfWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades.pdfapplication/pdf953252https://patua.iec.gov.br/bitstreams/f86b683e-51ef-407a-9735-7d51e2728a99/download655d9908b648a93e23b2a3df3487579fMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-871https://patua.iec.gov.br/bitstreams/0300be47-a1d1-485d-a2d5-5513da0184f0/download52f1732ea66fbd1123abe39f5373b797MD52TEXTWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades.pdf.txtWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades.pdf.txtExtracted texttext/plain73721https://patua.iec.gov.br/bitstreams/479cbd66-7eb5-4566-87e5-30f6d689f175/downloadca917f0da2d75cd6420a1ed7917b6cd2MD55THUMBNAILWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades.pdf.jpgWhole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades.pdf.jpgGenerated Thumbnailimage/jpeg5610https://patua.iec.gov.br/bitstreams/83decd4d-3c84-4e71-87e9-3992434f44f3/download9eab46e57a4fe159505f3fcef60dc082MD56iec/35152022-10-20 21:32:34.768oai:patua.iec.gov.br:iec/3515https://patua.iec.gov.brRepositório InstitucionalPUBhttps://patua.iec.gov.br/oai/requestclariceneta@iec.gov.br || Biblioteca@iec.gov.bropendoar:2022-10-20T21:32:34Repositório Digital do Instituto Evandro Chagas (Patuá) - Instituto Evandro Chagas (IEC)falseVG9kb3Mgb3MgZG9jdW1lbnRvcyBkZXNzYSBjb2xlw6fDo28gc2VndWVtIGEgTGljZW7Dp2EgQ3JlYXRpdmUgY29tbW9ucy4=
dc.title.pt_BR.fl_str_mv Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
title Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
spellingShingle Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
Vialle, Ricardo Assunção
Peixes / anatomia & histologia
Peixes / genética
Genoma / fisiologia
Mapeamento Cromossômico / métodos
Bacia do Rio Amazonas (BR)
Pirarucu
Arapaima gigas
title_short Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
title_full Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
title_fullStr Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
title_full_unstemmed Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
title_sort Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
author Vialle, Ricardo Assunção
author_facet Vialle, Ricardo Assunção
Souza, Jorge Estefano Santana de
Lopes, Katia de Paiva
Teixeira, Diego Gomes
Alves Sobrinho, Pitágoras de Azevedo
Ribeiro-dos-Santos, André M
Furtado, Carolina
Sakamoto, Tetsu
Silva, Fábio Augusto Oliveira
Oliveira, Edivaldo Herculano Correa de
Hamoy, Igor Guerreiro
Assumpção, Paulo Pimentel
Ribeiro-dos-Santos, Ândrea
Lima, João Paulo Mattos Santos
Seuánez, Héctor N
Souza, Sandro José de
Santos, Sidney
author_role author
author2 Souza, Jorge Estefano Santana de
Lopes, Katia de Paiva
Teixeira, Diego Gomes
Alves Sobrinho, Pitágoras de Azevedo
Ribeiro-dos-Santos, André M
Furtado, Carolina
Sakamoto, Tetsu
Silva, Fábio Augusto Oliveira
Oliveira, Edivaldo Herculano Correa de
Hamoy, Igor Guerreiro
Assumpção, Paulo Pimentel
Ribeiro-dos-Santos, Ândrea
Lima, João Paulo Mattos Santos
Seuánez, Héctor N
Souza, Sandro José de
Santos, Sidney
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Vialle, Ricardo Assunção
Souza, Jorge Estefano Santana de
Lopes, Katia de Paiva
Teixeira, Diego Gomes
Alves Sobrinho, Pitágoras de Azevedo
Ribeiro-dos-Santos, André M
Furtado, Carolina
Sakamoto, Tetsu
Silva, Fábio Augusto Oliveira
Oliveira, Edivaldo Herculano Correa de
Hamoy, Igor Guerreiro
Assumpção, Paulo Pimentel
Ribeiro-dos-Santos, Ândrea
Lima, João Paulo Mattos Santos
Seuánez, Héctor N
Souza, Sandro José de
Santos, Sidney
dc.subject.decsPrimary.pt_BR.fl_str_mv Peixes / anatomia & histologia
Peixes / genética
Genoma / fisiologia
Mapeamento Cromossômico / métodos
Bacia do Rio Amazonas (BR)
Pirarucu
Arapaima gigas
topic Peixes / anatomia & histologia
Peixes / genética
Genoma / fisiologia
Mapeamento Cromossômico / métodos
Bacia do Rio Amazonas (BR)
Pirarucu
Arapaima gigas
description The Pirarucu (Arapaima gigas) is one of the world’s largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.
publishDate 2018
dc.date.accessioned.fl_str_mv 2018-10-22T13:40:27Z
dc.date.available.fl_str_mv 2018-10-22T13:40:27Z
dc.date.issued.fl_str_mv 2018
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dc.identifier.citation.fl_str_mv VIALLE, Ricardo Assunção et al. Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades. Genome Biology and evolution, v. 10, n. 9, p. 2366-2379, Sept. 2018.
dc.identifier.uri.fl_str_mv https://patua.iec.gov.br/handle/iec/3515
dc.identifier.issn.-.fl_str_mv 1759-6653
dc.identifier.doi.-.fl_str_mv 10.1093/gbe/evy130
identifier_str_mv VIALLE, Ricardo Assunção et al. Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades. Genome Biology and evolution, v. 10, n. 9, p. 2366-2379, Sept. 2018.
1759-6653
10.1093/gbe/evy130
url https://patua.iec.gov.br/handle/iec/3515
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