Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate-Invertebrate Gap

• Tipo: Artigo em Revista Científica Internacional
• Data: 2013

Autores

Philippe Gayral (Autor) Outra; Jose Melo Ferreira (Autor) Outra; Sylvain Glemin (Autor) Outra; Nicolas Bierne (Autor) Outra; Miguel Carneiro (Autor) Outra; Benoit Nabholz (Autor) Outra; Joao M Lourenco (Autor) Outra; Paulo C Alves (Autor) FCUP; Marion Ballenghien (Autor) Outra; Nicolas Faivre (Autor) Outra; Khalid Belkhir (Autor) Outra; Vincent Cahais (Autor) Outra; Etienne Loire (Autor) Outra; Aurelien Bernard (Autor) Outra; Nicolas Galtier (Autor) Outra

Revista

Título: Plos Genetics

Vol. 9

Página Final: e1003457

ISSN: 1553-7390

Editora: Public Library of Science

Indexação

ISI Web of Knowledge - 127 Citações

Scopus - 127 Citações

Classificação Científica

FOS: Ciências exactas e naturais > Ciências da terra e ciências do ambiente

Outras Informações

ID Authenticus: P-005-1XN

DOI: 10.1371/journal.pgen.1003457

Abstract (EN): In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Nº de páginas: 15