title: Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.
abstract: 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.
authors.affiliation: Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Gayral
authors.forename: José
authors.initials: J
authors.lastname: Melo-Ferreira
authors.forename: Sylvain
authors.initials: S
authors.lastname: Glémin
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bierne
authors.forename: Miguel
authors.initials: M
authors.lastname: Carneiro
authors.forename: Benoit
authors.initials: B
authors.lastname: Nabholz
authors.forename: Joao M
authors.initials: JM
authors.lastname: Lourenco
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Alves
authors.forename: Marion
authors.initials: M
authors.lastname: Ballenghien
authors.forename: Nicolas
authors.initials: N
authors.lastname: Faivre
authors.forename: Khalid
authors.initials: K
authors.lastname: Belkhir
authors.forename: Vincent
authors.initials: V
authors.lastname: Cahais
authors.forename: Etienne
authors.initials: E
authors.lastname: Loire
authors.forename: Aurélien
authors.initials: A
authors.lastname: Bernard
authors.forename: Nicolas
authors.initials: N
authors.lastname: Galtier
mesh_terms: D000818:Animals; D001483:Base Sequence; D004330:Drosophila / Q000235:genetics*; D015894:Genome, Human; D005838:Genotype; D034621:Hares / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007448:Invertebrates / Q000235:genetics; D020049:Isoptera / Q000235:genetics; D056186:Metagenomics; D010125:Ostreidae / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome / Q000235:genetics*; D014426:Turtles / Q000235:genetics; D014561:Urochordata / Q000235:genetics; D014714:Vertebrates / Q000235:genetics