Data from: Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.

Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Aves: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as successive sister groups to this clade. This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes.Aligned and unaligned sequences use for phylogenetics analysesThe gene folder contains three type of files : 1) The *.fst files are unaligned nucleotides sequences 2) The *.mafft.fst are aligned amino-acid sequences 3) The *_base.fst are aligned nucleotides sequences corvusBrachyrhynchos, parusCaeruleus, manacusVitellinus, ficedulaHypoleuca sequences were obtained from brain transcriptome sequencing (see Nabholz B, Jarvis ED, Ellegren H. 2010. Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Mol. Phylogenet. Evol. 57:466–470)gene.zi