DNA barcoding of the rodent genusOligoryzomys(Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

Autor: Marcelo Weksler, Alexandra M. R. Bezerra, João Alves de Oliveira, Francisco Prosdocimi, Luiz Flamarion B. Oliveira, Cibele R. Bonvicino, Marcos de O.R. da Cruz, Claudia Regina Silva, Carolina Furtado, Lena Geise, Benoit de Thoisy, François Catzeflis
Přispěvatelé: Universidade Federal do Rio de Janeiro (UFRJ), Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Universidade do Estado do Rio de Janeiro [Rio de Janeiro] (UERJ), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université de Montpellier (UM)
Rok vydání: 2019
Předmět:
Zdroj: Mitochondrial DNA Part A
Mitochondrial DNA Part A, Taylor and Francis, 2019, 30 (5), pp.702-712. ⟨10.1080/24701394.2019.1622692⟩
ISSN: 2470-1408
2470-1394
Popis: International audience; DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.
Databáze: OpenAIRE
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