Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly

Abstract

The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

FIG. 1.—

Transcription of the mitochondrial genome of Drosophila melanogaster (after Berthier et al. 1986). Horizontal arrows indicate the extent of the primary transcripts. Vertical arrows indicate the positions of bidirectional attenuator sequences (Roberti et al. 2003). The short-dashed extensions indicate possible “bleed through” beyond the attenuator sequences.

FIG. 2.—

Sequence alignments of the two sites where primary transcripts from opposite strands meet. Due to a gene rearrangement, the junction in Paracladura (part B) is cytb–nad1, rather than trnS2–nad1. In Sylvicola (part A), some additional noncoding residues have been removed.

FIG. 3.—

N-strand sequence of the junction between the A + T rich region and the 5′ end of rrnS genes in Diptera and Mecoptera. The top line shows the 5′ end of the Drosophila melanogaster 12S rRNA.

FIG. 4.—

Gene arrangements in two species of winter crane fly (Family Trichoceridae). Trichocera bimaculata retains the ancestral dipteran arrangement. Paracladura trichoptera has undergone extensive rearrangement. Genes shown above each rectangle are transcribed from the majority strand. Those below the rectangles are transcribed from the minority strand.

FIG. 5.—

Hypothesis to explain the rearrangements observed in Paracladura. (A) Ancestral arrangement; (B) Hypothetical intermediate after complete genome duplication; (C) Gene arrangement in Paracladura. Most of the tRNA genes are omitted for simplicity. Horizontal arrows in parts A and B show the probable positions of primary transcripts. Transcripts D and C′ (part B) have no apparent coding function in Paracladura as indicated by crosses on each arrow.

FIG. 6.—

A mitochondrial phylogenetic tree of major groups of Diptera. The tree is derived from a Bayesian analysis of all major genes, using codon positions 1 and 2 for protein coding genes, and all alignable sites for the ribosomal genes. Numbers above the branches are credibility scores. The tree is rooted with taxa from the related Order Mecoptera (Scorpion flies).

FIG. 7.—

A Bayesian mitochondrial tree using codon positions 1 and 2 for cox1–3, cytb, and atp6 genes, and all alignable sites for the ribosomal genes. Numbers above the branches are credibility scores. Numbers below the branches are neighbor joining bootstraps. The tree is rooted with the Mecoptera.

FIG. 8.—

Neighbor joining tree using the same data set as Figure 7, showing the branch lengths. Numbers adjacent to each node are bootstraps.