Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1007/s00438-016-1176-1 http://hdl.handle.net/11449/177782 |
Resumo: | Integration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics. |
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Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticusBioinformaticsDNA mappingGenomic organizationRepeated DNAIntegration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics.Department of Bioprocess and Biotechnology Faculty of Agronomic Sciences UNESP Sao Paulo State UniversityUniversity of Maryland, Bioscience Research BuildingDepartment of Biology University of RochesterMorphology Department Institute of Biosciences UNESP Sao Paulo State UniversityDepartment of Bioprocess and Biotechnology Faculty of Agronomic Sciences UNESP Sao Paulo State UniversityMorphology Department Institute of Biosciences UNESP Sao Paulo State UniversityUniversidade Estadual Paulista (Unesp)University of MarylandUniversity of RochesterValente, Guilherme [UNESP]Kocher, ThomasEickbush, ThomasSimões, Rafael P. [UNESP]Martins, Cesar [UNESP]2018-12-11T17:27:05Z2018-12-11T17:27:05Z2016-06-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1219-1225application/pdfhttp://dx.doi.org/10.1007/s00438-016-1176-1Molecular Genetics and Genomics, v. 291, n. 3, p. 1219-1225, 2016.1617-46231617-4615http://hdl.handle.net/11449/17778210.1007/s00438-016-1176-12-s2.0-849576250462-s2.0-84957625046.pdf186281482759063288588006994253520000-0002-3433-85740000-0003-3534-974XScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Genetics and Genomics1,1681,168info:eu-repo/semantics/openAccess2024-01-29T06:24:42Zoai:repositorio.unesp.br:11449/177782Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-06T00:11:38.168163Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
title |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
spellingShingle |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus Valente, Guilherme [UNESP] Bioinformatics DNA mapping Genomic organization Repeated DNA |
title_short |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
title_full |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
title_fullStr |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
title_full_unstemmed |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
title_sort |
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus |
author |
Valente, Guilherme [UNESP] |
author_facet |
Valente, Guilherme [UNESP] Kocher, Thomas Eickbush, Thomas Simões, Rafael P. [UNESP] Martins, Cesar [UNESP] |
author_role |
author |
author2 |
Kocher, Thomas Eickbush, Thomas Simões, Rafael P. [UNESP] Martins, Cesar [UNESP] |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) University of Maryland University of Rochester |
dc.contributor.author.fl_str_mv |
Valente, Guilherme [UNESP] Kocher, Thomas Eickbush, Thomas Simões, Rafael P. [UNESP] Martins, Cesar [UNESP] |
dc.subject.por.fl_str_mv |
Bioinformatics DNA mapping Genomic organization Repeated DNA |
topic |
Bioinformatics DNA mapping Genomic organization Repeated DNA |
description |
Integration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-06-01 2018-12-11T17:27:05Z 2018-12-11T17:27:05Z |
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/s00438-016-1176-1 Molecular Genetics and Genomics, v. 291, n. 3, p. 1219-1225, 2016. 1617-4623 1617-4615 http://hdl.handle.net/11449/177782 10.1007/s00438-016-1176-1 2-s2.0-84957625046 2-s2.0-84957625046.pdf 1862814827590632 8858800699425352 0000-0002-3433-8574 0000-0003-3534-974X |
url |
http://dx.doi.org/10.1007/s00438-016-1176-1 http://hdl.handle.net/11449/177782 |
identifier_str_mv |
Molecular Genetics and Genomics, v. 291, n. 3, p. 1219-1225, 2016. 1617-4623 1617-4615 10.1007/s00438-016-1176-1 2-s2.0-84957625046 2-s2.0-84957625046.pdf 1862814827590632 8858800699425352 0000-0002-3433-8574 0000-0003-3534-974X |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Molecular Genetics and Genomics 1,168 1,168 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1219-1225 application/pdf |
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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1808129593482149888 |