De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes

Detalhes bibliográficos
Autor(a) principal: Jehangir, Maryam [UNESP]
Data de Publicação: 2019
Outros Autores: Ahmad, Syed F. [UNESP], Cardoso, Adauto L. [UNESP], Ramos, Erica [UNESP], Valente, Guilherme T. [UNESP], Martins, Cesar [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1007/s00412-019-00707-7
http://hdl.handle.net/11449/189166
Resumo: Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.
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spelling De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomesChromosome rearrangementCichlid fishExtra chromosomeGenome evolutionNext-generation sequencingSupernumerary chromosomeSupernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.Department of Morphology Institute of Bioscience at Botucatu São Paulo State University – UNESPBioprocess and Biotechnology Department Agronomical Science Faculty Sao Paulo State University – UNESPDepartment of Morphology Institute of Bioscience at Botucatu São Paulo State University – UNESPBioprocess and Biotechnology Department Agronomical Science Faculty Sao Paulo State University – UNESPUniversidade Estadual Paulista (Unesp)Jehangir, Maryam [UNESP]Ahmad, Syed F. [UNESP]Cardoso, Adauto L. [UNESP]Ramos, Erica [UNESP]Valente, Guilherme T. [UNESP]Martins, Cesar [UNESP]2019-10-06T16:31:55Z2019-10-06T16:31:55Z2019-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1007/s00412-019-00707-7Chromosoma.1432-08860009-5915http://hdl.handle.net/11449/18916610.1007/s00412-019-00707-72-s2.0-8506612511488588006994253520000-0003-3534-974XScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengChromosomainfo:eu-repo/semantics/openAccess2021-10-23T22:14:29Zoai:repositorio.unesp.br:11449/189166Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:21:36.488436Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
title De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
spellingShingle De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
Jehangir, Maryam [UNESP]
Chromosome rearrangement
Cichlid fish
Extra chromosome
Genome evolution
Next-generation sequencing
Supernumerary chromosome
title_short De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
title_full De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
title_fullStr De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
title_full_unstemmed De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
title_sort De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
author Jehangir, Maryam [UNESP]
author_facet Jehangir, Maryam [UNESP]
Ahmad, Syed F. [UNESP]
Cardoso, Adauto L. [UNESP]
Ramos, Erica [UNESP]
Valente, Guilherme T. [UNESP]
Martins, Cesar [UNESP]
author_role author
author2 Ahmad, Syed F. [UNESP]
Cardoso, Adauto L. [UNESP]
Ramos, Erica [UNESP]
Valente, Guilherme T. [UNESP]
Martins, Cesar [UNESP]
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Jehangir, Maryam [UNESP]
Ahmad, Syed F. [UNESP]
Cardoso, Adauto L. [UNESP]
Ramos, Erica [UNESP]
Valente, Guilherme T. [UNESP]
Martins, Cesar [UNESP]
dc.subject.por.fl_str_mv Chromosome rearrangement
Cichlid fish
Extra chromosome
Genome evolution
Next-generation sequencing
Supernumerary chromosome
topic Chromosome rearrangement
Cichlid fish
Extra chromosome
Genome evolution
Next-generation sequencing
Supernumerary chromosome
description Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.
publishDate 2019
dc.date.none.fl_str_mv 2019-10-06T16:31:55Z
2019-10-06T16:31:55Z
2019-01-01
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/10.1007/s00412-019-00707-7
Chromosoma.
1432-0886
0009-5915
http://hdl.handle.net/11449/189166
10.1007/s00412-019-00707-7
2-s2.0-85066125114
8858800699425352
0000-0003-3534-974X
url http://dx.doi.org/10.1007/s00412-019-00707-7
http://hdl.handle.net/11449/189166
identifier_str_mv Chromosoma.
1432-0886
0009-5915
10.1007/s00412-019-00707-7
2-s2.0-85066125114
8858800699425352
0000-0003-3534-974X
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Chromosoma
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
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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