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The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system

Bibliographic Details
Main Author: Wolf, Ivan Rodrigo
Publication Date: 2024
Other Authors: Schemberger, Michelle Orane, Azambuja, Matheus, Oliveira, Fernanda Souza, Nogaroto, Viviane, Valente, Guilherme Targino, Martins, Cesar, Vicari, Marcelo Ricardo
Format: Article
Language: eng
Source: Repositório Institucional da FIOCRUZ (ARCA)
DOI: 10.1590/1678-4685-GMB-2024-0098
Download full: https://arca.fiocruz.br/handle/icict/67598
Summary: This study was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo, grant number: 2015/16661-1), Fundação Araucária (Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Estado do Paraná, grant number: 9/2017), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Finance Code 001), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, grant number: 313566/2023-2). The authors are also grateful to Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio, license number 15117) for authorizing the collection of specimens.
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spelling Wolf, Ivan RodrigoSchemberger, Michelle OraneAzambuja, MatheusOliveira, Fernanda SouzaNogaroto, VivianeValente, Guilherme TarginoMartins, CesarVicari, Marcelo Ricardo2024-12-14T13:10:57Z2024-12-14T13:10:57Z2024WOLF, I. R. et al. The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system. Genetics and Molecular Biology, v. 47, n. 4 (e20240098), p. 1-6, 2024.1678-4685https://arca.fiocruz.br/handle/icict/6759810.1590/1678-4685-GMB-2024-0098This study was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo, grant number: 2015/16661-1), Fundação Araucária (Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Estado do Paraná, grant number: 9/2017), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Finance Code 001), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, grant number: 313566/2023-2). The authors are also grateful to Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio, license number 15117) for authorizing the collection of specimens.Universidade Estadual Paulista. Instituto de Biociências de Botucatu. Departamento de Morfologia. Botucatu, SP, Brasil.Universidade Federal do Paraná. Centro Politécnico. Programa de Pós-Graduação em Genética. Curitiba, PR, Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório da Regulação da Expressão Gênica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Centro Politécnico. Programa de Pós-Graduação em Genética. Curitiba, PR, Brasil.Universidade Federal do Paraná. Centro Politécnico. Programa de Pós-Graduação em Genética. Curitiba, PR, Brasil.Universidade Estadual de Ponta Grossa. Departamento de Biologia Estrutural, Molecular e Genética. Ponta Grossa, PR, Brasil.Universidade Estadual Paulista. Instituto de Biociências de Botucatu. Departamento de Morfologia. Botucatu, SP, Brasil.Universidade Estadual Paulista. Instituto de Biociências de Botucatu. Departamento de Morfologia. Botucatu, SP, Brasil.Universidade Federal do Paraná. Centro Politécnico. Programa de Pós-Graduação em Genética. Curitiba, PR, Brasil / Universidade Estadual de Ponta Grossa. Departamento de Biologia Estrutural, Molecular e Genética. Ponta Grossa, PR, Brasil.Neotropical fishes emerge as an extremely diverse group of vertebrates where genomic strategies to evaluate structural and functional features are still beginning. Here, we present a second draft genome of Apareiodon sp. (2n=54, ZZ/ZW), adding PacBio technology whole genome sequencing, and assembling by combining two technologies (long and short reads). Using a detailed strategy for genome assembly with fish genomes of Pygocentrus nattereri, Carassius auratus, and Astyanax mexicanus as references, the final assembly of the Apareiodon sp. genome generated 93 scaffolds, an N50 of 37,200,078 bases, and a size estimate considering 28 scaffolds (26 autosomes+ZW) of ~945 Mb. In Apareiodon sp., this second genome draft confirmed that ~36% of the genome is composed of repetitive DNA. Furthermore, the new draft genome has improved genomic quality assessments, allowing the annotation of 36,290 genes and 15,683 proteins, which presented similarities to reference genomes. The second draft genome of Apareiodon sp. will be useful for research on integrative cytogenetic and genomic data. It will open perspectives for analyzing sex-determining genes in Neotropical fish with a ZZ/ZW sex chromosome system.engSociedade Brasileira de GenéticaCromossomosSequência genômicaChromosomesGenome sequenceParodontidaeTeleosteiCromossomosSequenciamento Completo do GenomaThe long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome systeminfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://arca.fiocruz.br/bitstreams/70764574-8148-472e-9993-2f159c41ef7a/download5a560609d32a3863062d77ff32785d58MD51falseAnonymousREADORIGINALve_Ivan_Wolf_etal_ICC_2024.pdfve_Ivan_Wolf_etal_ICC_2024.pdfapplication/pdf1812890https://arca.fiocruz.br/bitstreams/539d8192-d0dd-47fc-b87e-778e12c6a5aa/downloadaa8a3f2478b9447ab4985a76cfc789b4MD52trueAnonymousREADTEXTve_Ivan_Wolf_etal_ICC_2024.pdf.txtve_Ivan_Wolf_etal_ICC_2024.pdf.txtExtracted texttext/plain23840https://arca.fiocruz.br/bitstreams/d5f5173f-cbae-4da7-98a5-998b94e91a20/download06f2f9e16e28b74e24bd7bfaf1306308MD55falseAnonymousREADTHUMBNAILve_Ivan_Wolf_etal_ICC_2024.pdf.jpgve_Ivan_Wolf_etal_ICC_2024.pdf.jpgGenerated Thumbnailimage/jpeg5849https://arca.fiocruz.br/bitstreams/348d7b15-c0b9-4146-bb4e-0c7ca27a3d59/downloade4e01c84350d3eaa46d29ea3eb9fe830MD56falseAnonymousREADicict/675982025-07-29 23:21:37.005open.accessoai:arca.fiocruz.br:icict/67598https://arca.fiocruz.brRepositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352025-07-30T02:21:37Repositório Institucional da FIOCRUZ (ARCA) - 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dc.title.none.fl_str_mv The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
title The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
spellingShingle The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
Wolf, Ivan Rodrigo
Cromossomos
Sequência genômica
Chromosomes
Genome sequence
Parodontidae
Teleostei
Cromossomos
Sequenciamento Completo do Genoma
title_short The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
title_full The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
title_fullStr The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
title_full_unstemmed The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
title_sort The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system
author Wolf, Ivan Rodrigo
author_facet Wolf, Ivan Rodrigo
Schemberger, Michelle Orane
Azambuja, Matheus
Oliveira, Fernanda Souza
Nogaroto, Viviane
Valente, Guilherme Targino
Martins, Cesar
Vicari, Marcelo Ricardo
author_role author
author2 Schemberger, Michelle Orane
Azambuja, Matheus
Oliveira, Fernanda Souza
Nogaroto, Viviane
Valente, Guilherme Targino
Martins, Cesar
Vicari, Marcelo Ricardo
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Wolf, Ivan Rodrigo
Schemberger, Michelle Orane
Azambuja, Matheus
Oliveira, Fernanda Souza
Nogaroto, Viviane
Valente, Guilherme Targino
Martins, Cesar
Vicari, Marcelo Ricardo
dc.subject.other.none.fl_str_mv Cromossomos
Sequência genômica
topic Cromossomos
Sequência genômica
Chromosomes
Genome sequence
Parodontidae
Teleostei
Cromossomos
Sequenciamento Completo do Genoma
dc.subject.en.none.fl_str_mv Chromosomes
Genome sequence
Parodontidae
Teleostei
dc.subject.decs.none.fl_str_mv Cromossomos
Sequenciamento Completo do Genoma
description This study was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo, grant number: 2015/16661-1), Fundação Araucária (Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Estado do Paraná, grant number: 9/2017), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Finance Code 001), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, grant number: 313566/2023-2). The authors are also grateful to Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio, license number 15117) for authorizing the collection of specimens.
publishDate 2024
dc.date.accessioned.fl_str_mv 2024-12-14T13:10:57Z
dc.date.available.fl_str_mv 2024-12-14T13:10:57Z
dc.date.issued.fl_str_mv 2024
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.citation.fl_str_mv WOLF, I. R. et al. The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system. Genetics and Molecular Biology, v. 47, n. 4 (e20240098), p. 1-6, 2024.
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/67598
dc.identifier.issn.none.fl_str_mv 1678-4685
dc.identifier.doi.none.fl_str_mv 10.1590/1678-4685-GMB-2024-0098
identifier_str_mv WOLF, I. R. et al. The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system. Genetics and Molecular Biology, v. 47, n. 4 (e20240098), p. 1-6, 2024.
1678-4685
10.1590/1678-4685-GMB-2024-0098
url https://arca.fiocruz.br/handle/icict/67598
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Sociedade Brasileira de Genética
publisher.none.fl_str_mv Sociedade Brasileira de Genética
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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