Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.

Detalhes bibliográficos
Autor(a) principal: PESSOA FILHO, M. A. C. de P.
Data de Publicação: 2017
Outros Autores: MARTINS, A. M., FERREIRA, M. E.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072837
Resumo: Abstract: Background: Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels). Results: Whole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya. Conclusion: Low-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.
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spelling Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.BrachiariaCapim UrochloaGramínea ForrageiraAbstract: Background: Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels). Results: Whole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya. Conclusion: Low-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.MARCO AURELIO CALDAS DE PINHO PESSO, CPAC; ALEXANDRE MAGALHÃES MARTINS, CAPES; MARCIO ELIAS FERREIRA, SRI.PESSOA FILHO, M. A. C. de P.MARTINS, A. M.FERREIRA, M. E.2017-07-18T11:11:11Z2017-07-18T11:11:11Z2017-07-1820172017-08-11T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article14 p.BMC Genomics, v. 18, n. 516, 2017.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072837DOI 10.1186/s12864-017-3904-2enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-08-16T04:37:08Zoai:www.alice.cnptia.embrapa.br:doc/1072837Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-08-16T04:37:08Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
title Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
spellingShingle Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
PESSOA FILHO, M. A. C. de P.
Brachiaria
Capim Urochloa
Gramínea Forrageira
title_short Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
title_full Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
title_fullStr Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
title_full_unstemmed Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
title_sort Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes.
author PESSOA FILHO, M. A. C. de P.
author_facet PESSOA FILHO, M. A. C. de P.
MARTINS, A. M.
FERREIRA, M. E.
author_role author
author2 MARTINS, A. M.
FERREIRA, M. E.
author2_role author
author
dc.contributor.none.fl_str_mv MARCO AURELIO CALDAS DE PINHO PESSO, CPAC; ALEXANDRE MAGALHÃES MARTINS, CAPES; MARCIO ELIAS FERREIRA, SRI.
dc.contributor.author.fl_str_mv PESSOA FILHO, M. A. C. de P.
MARTINS, A. M.
FERREIRA, M. E.
dc.subject.por.fl_str_mv Brachiaria
Capim Urochloa
Gramínea Forrageira
topic Brachiaria
Capim Urochloa
Gramínea Forrageira
description Abstract: Background: Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels). Results: Whole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya. Conclusion: Low-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.
publishDate 2017
dc.date.none.fl_str_mv 2017-07-18T11:11:11Z
2017-07-18T11:11:11Z
2017-07-18
2017
2017-08-11T11:11:11Z
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 BMC Genomics, v. 18, n. 516, 2017.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072837
DOI 10.1186/s12864-017-3904-2
identifier_str_mv BMC Genomics, v. 18, n. 516, 2017.
DOI 10.1186/s12864-017-3904-2
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072837
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.format.none.fl_str_mv 14 p.
dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
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instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
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collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
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repository.mail.fl_str_mv cg-riaa@embrapa.br
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