Your browser doesn't support javascript.
loading
Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data.
Vargas, Oscar M; Heuertz, Myriam; Smith, Stephen A; Dick, Christopher W.
Afiliação
  • Vargas OM; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: oscarvargash@gmail.com.
  • Heuertz M; Biogeco, INRA, Univ. Bordeaux, F-33610 Cestas, France.
  • Smith SA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
  • Dick CW; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama.
Mol Phylogenet Evol ; 135: 98-104, 2019 06.
Article em En | MEDLINE | ID: mdl-30818022
Reconstructing species trees from multi-loci datasets is becoming a standard practice in phylogenetics. Nevertheless, access to high-throughput sequencing may be costly, especially with studies of many samples. The potential high cost makes a priori assessments desirable in order to make informed decisions about sequencing. We generated twelve transcriptomes for ten species of the Brazil nut family (Lecythidaceae), identified a set of putatively orthologous nuclear loci and evaluated, in silico, their phylogenetic utility using genome skimming data of 24 species. We designed the markers using MarkerMiner, and developed a script, GoldFinder, to efficiently sub-select the best makers for sequencing. We captured, in silico, all designed 354 nuclear loci and performed a maximum likelihood phylogenetic analysis on the concatenated sequence matrix. We also calculated individual gene trees with maximum likelihood and used them for a coalescent-based species tree inference. Both analyses resulted in almost identical topologies. However, our nuclear-loci phylogenies were strongly incongruent with a published plastome phylogeny, suggesting that plastome data alone is not sufficient for species tree estimation. Our results suggest that using hundreds of nuclear markers (i.e. 354) will significantly improve the Lecythidaceae species tree. The framework described here will be useful, generally, for developing markers for species tree inference.
Assuntos
Palavras-chave
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Seleção Genética / Simulação por Computador / Análise de Sequência de DNA / Genoma de Planta / Bertholletia Tipo de estudo: Prognostic_studies País/Região como assunto: America do sul / Brasil Idioma: En Revista: Mol Phylogenet Evol Assunto da revista: BIOLOGIA / BIOLOGIA MOLECULAR Ano de publicação: 2019 Tipo de documento: Article País de publicação: Estados Unidos
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Seleção Genética / Simulação por Computador / Análise de Sequência de DNA / Genoma de Planta / Bertholletia Tipo de estudo: Prognostic_studies País/Região como assunto: America do sul / Brasil Idioma: En Revista: Mol Phylogenet Evol Assunto da revista: BIOLOGIA / BIOLOGIA MOLECULAR Ano de publicação: 2019 Tipo de documento: Article País de publicação: Estados Unidos