The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha

PLoS One. 2015 Mar 31;10(3):e0123594. doi: 10.1371/journal.pone.0123594. eCollection 2015.

Abstract

Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Composition
  • Base Sequence
  • Codon
  • Diptera / classification
  • Diptera / genetics*
  • Genome, Mitochondrial*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny*
  • RNA, Ribosomal / genetics
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics

Substances

  • Codon
  • RNA, Ribosomal
  • RNA, Transfer

Grants and funding

DY was funded by the National Natural Science Foundation of China (31320103902) and the National "Twelfth Five-Year" Plan for Science and Technology Support (2012BAD19B00). SLC was funded by an Australian Research Council Future Fellowship (FT120100746). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.