Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap
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.
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dig-cirad-fr-5773252024-01-28T22:51:50Z http://agritrop.cirad.fr/577325/ http://agritrop.cirad.fr/577325/ Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap. Gayral Philippe, Melo-Ferreira José, Glemin Sylvain, Bierne Nicolas, Carneiro Miguel, Nabholz Benoit, Lourenco Joao M., Alves Paulo, Ballenghien Marion, Faivre Nicolas, Belkhir Khalid, Cahais Vincent, Loire Etienne, Bernard Aurélien, Galtier Nicolas. 2013. PLoS Genetics, 9 (4):e1003457, 15 p.https://doi.org/10.1371/journal.pgen.1003457 <https://doi.org/10.1371/journal.pgen.1003457> Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap Gayral, Philippe Melo-Ferreira, José Glemin, Sylvain Bierne, Nicolas Carneiro, Miguel Nabholz, Benoit Lourenco, Joao M. Alves, Paulo Ballenghien, Marion Faivre, Nicolas Belkhir, Khalid Cahais, Vincent Loire, Etienne Bernard, Aurélien Galtier, Nicolas eng 2013 PLoS Genetics L10 - Génétique et amélioration des animaux U30 - Méthodes de recherche génomique génie génétique modèle animal génétique des populations population animale Invertébré mammifère Ostrea lièvre Reticulitermes Emydidae étude de cas méthodologie taille du groupe http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_34782 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_435 http://aims.fao.org/aos/agrovoc/c_3929 http://aims.fao.org/aos/agrovoc/c_4560 http://aims.fao.org/aos/agrovoc/c_5447 http://aims.fao.org/aos/agrovoc/c_3496 http://aims.fao.org/aos/agrovoc/c_6537 http://aims.fao.org/aos/agrovoc/c_32575 http://aims.fao.org/aos/agrovoc/c_24392 http://aims.fao.org/aos/agrovoc/c_12522 http://aims.fao.org/aos/agrovoc/c_24852 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/577325/1/journal.pgen.1003457.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1371/journal.pgen.1003457 10.1371/journal.pgen.1003457 info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pgen.1003457 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1371/journal.pgen.1003457 |
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L10 - Génétique et amélioration des animaux U30 - Méthodes de recherche génomique génie génétique modèle animal génétique des populations population animale Invertébré mammifère Ostrea lièvre Reticulitermes Emydidae étude de cas méthodologie taille du groupe http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_34782 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_435 http://aims.fao.org/aos/agrovoc/c_3929 http://aims.fao.org/aos/agrovoc/c_4560 http://aims.fao.org/aos/agrovoc/c_5447 http://aims.fao.org/aos/agrovoc/c_3496 http://aims.fao.org/aos/agrovoc/c_6537 http://aims.fao.org/aos/agrovoc/c_32575 http://aims.fao.org/aos/agrovoc/c_24392 http://aims.fao.org/aos/agrovoc/c_12522 http://aims.fao.org/aos/agrovoc/c_24852 L10 - Génétique et amélioration des animaux U30 - Méthodes de recherche génomique génie génétique modèle animal génétique des populations population animale Invertébré mammifère Ostrea lièvre Reticulitermes Emydidae étude de cas méthodologie taille du groupe http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_34782 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_435 http://aims.fao.org/aos/agrovoc/c_3929 http://aims.fao.org/aos/agrovoc/c_4560 http://aims.fao.org/aos/agrovoc/c_5447 http://aims.fao.org/aos/agrovoc/c_3496 http://aims.fao.org/aos/agrovoc/c_6537 http://aims.fao.org/aos/agrovoc/c_32575 http://aims.fao.org/aos/agrovoc/c_24392 http://aims.fao.org/aos/agrovoc/c_12522 http://aims.fao.org/aos/agrovoc/c_24852 |
spellingShingle |
L10 - Génétique et amélioration des animaux U30 - Méthodes de recherche génomique génie génétique modèle animal génétique des populations population animale Invertébré mammifère Ostrea lièvre Reticulitermes Emydidae étude de cas méthodologie taille du groupe http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_34782 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_435 http://aims.fao.org/aos/agrovoc/c_3929 http://aims.fao.org/aos/agrovoc/c_4560 http://aims.fao.org/aos/agrovoc/c_5447 http://aims.fao.org/aos/agrovoc/c_3496 http://aims.fao.org/aos/agrovoc/c_6537 http://aims.fao.org/aos/agrovoc/c_32575 http://aims.fao.org/aos/agrovoc/c_24392 http://aims.fao.org/aos/agrovoc/c_12522 http://aims.fao.org/aos/agrovoc/c_24852 L10 - Génétique et amélioration des animaux U30 - Méthodes de recherche génomique génie génétique modèle animal génétique des populations population animale Invertébré mammifère Ostrea lièvre Reticulitermes Emydidae étude de cas méthodologie taille du groupe http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_34782 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_435 http://aims.fao.org/aos/agrovoc/c_3929 http://aims.fao.org/aos/agrovoc/c_4560 http://aims.fao.org/aos/agrovoc/c_5447 http://aims.fao.org/aos/agrovoc/c_3496 http://aims.fao.org/aos/agrovoc/c_6537 http://aims.fao.org/aos/agrovoc/c_32575 http://aims.fao.org/aos/agrovoc/c_24392 http://aims.fao.org/aos/agrovoc/c_12522 http://aims.fao.org/aos/agrovoc/c_24852 Gayral, Philippe Melo-Ferreira, José Glemin, Sylvain Bierne, Nicolas Carneiro, Miguel Nabholz, Benoit Lourenco, Joao M. Alves, Paulo Ballenghien, Marion Faivre, Nicolas Belkhir, Khalid Cahais, Vincent Loire, Etienne Bernard, Aurélien Galtier, Nicolas Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
description |
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. |
format |
article |
topic_facet |
L10 - Génétique et amélioration des animaux U30 - Méthodes de recherche génomique génie génétique modèle animal génétique des populations population animale Invertébré mammifère Ostrea lièvre Reticulitermes Emydidae étude de cas méthodologie taille du groupe http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_34782 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_435 http://aims.fao.org/aos/agrovoc/c_3929 http://aims.fao.org/aos/agrovoc/c_4560 http://aims.fao.org/aos/agrovoc/c_5447 http://aims.fao.org/aos/agrovoc/c_3496 http://aims.fao.org/aos/agrovoc/c_6537 http://aims.fao.org/aos/agrovoc/c_32575 http://aims.fao.org/aos/agrovoc/c_24392 http://aims.fao.org/aos/agrovoc/c_12522 http://aims.fao.org/aos/agrovoc/c_24852 |
author |
Gayral, Philippe Melo-Ferreira, José Glemin, Sylvain Bierne, Nicolas Carneiro, Miguel Nabholz, Benoit Lourenco, Joao M. Alves, Paulo Ballenghien, Marion Faivre, Nicolas Belkhir, Khalid Cahais, Vincent Loire, Etienne Bernard, Aurélien Galtier, Nicolas |
author_facet |
Gayral, Philippe Melo-Ferreira, José Glemin, Sylvain Bierne, Nicolas Carneiro, Miguel Nabholz, Benoit Lourenco, Joao M. Alves, Paulo Ballenghien, Marion Faivre, Nicolas Belkhir, Khalid Cahais, Vincent Loire, Etienne Bernard, Aurélien Galtier, Nicolas |
author_sort |
Gayral, Philippe |
title |
Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
title_short |
Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
title_full |
Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
title_fullStr |
Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
title_full_unstemmed |
Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
title_sort |
reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap |
url |
http://agritrop.cirad.fr/577325/ http://agritrop.cirad.fr/577325/1/journal.pgen.1003457.pdf |
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