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.
Nabholz
Benoit
B
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. benoit.nabholz@ebc.uu.se
Jarvis
Erich D
ED
Ellegren
Hans
H
D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D054629:Genome, Mitochondrial; D046109:Passeriformes / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods
D004272:DNA, Mitochondrial