Evolution of the mitochondrial genomes of gall midges (Diptera: Cecidomyiidae): rearrangement and severe truncation of tRNA genes

Abstract

We determined the complete mitochondrial genome sequences of two species of gall midges (Diptera: Cecidomyiidae), as well as partial sequence from a third cecidomyiid and a species from a related family, the Sciaridae. The sciarid sequence has a number of rearrangements of tRNA genes, relative to other dipterans, but is otherwise unremarkable. In contrast, the cecidomyiid genomes possess a number of very unusual features. First, the two complete sequences are very small compared with other dipteran mitochondrial genomes. The genome of Mayetiola destructor is only 14,759 bp while that of Rhopalomyia pomum is only 14,503 bp, comparable with genome sizes observed in some arachnids. Second, all three cecidomyiid species have very high A + T content--more than 83% for the coding region. Third, all three cecidomyiid species possess a number of rearrangements of tRNA genes, including variations within the family. Fourth, the most extraordinary feature of cecidomyiids examined in this study is an extreme truncation of all tRNA genes, including the loss of TPsiC arms and apparent absence of the 3' part of the aminoacyl stems.The truncated tRNA genes of cecidomyiids are very similar to those previously reported for spiders and appear to represent a second, independent origin of these structural features. It is likely that they are made functional through RNA editing, perhaps using the 5' end of the aminoacyl stem as a template for the construction of the required 3' end.

Keywords: Mayetiola destructor; RNA editing; truncated tRNA genes.

FIG. 1.—

Organization of the mitochondrial genomes of representatives of the families Cecidomyiidae and Sciaridae. The genome structures are linearized to place the control region at the end. The “typical” gene order is that found in Drosophila and is widespread in insects. The upper line of gene names are coded on the majority (J) strand; the lower line gives those coded on the minority (N) strand. Protein-coding genes: A6, A8 are ATPase subunits 6 and 8; C1–C3 are cytochrome oxidase subunits; CB is cytochrome B; and N1–N6 and N4L are NADH dehydrogenase subunits. Ribosomal genes: 16s and 12s are the large and small subunits. The tRNA genes are indicated by their single-letter amino acid designations. Lines indicate transpositions; curved arrows indicate that an inversion is involved. Question marks indicate tRNA genes not present in their typical positions and assumed to have transposed into regions not sequenced.

FIG. 2.—

Comparison of tRNA gene sequences in cecidomyiids. The Mayetiola sequence is given for each group, while sequences of Rhopalomyia and Asphondylia are compared below, with dots indicating identical residues and dashes indicating indels. In the top line of each grouping, dots indicate pairing regions; the first two groups of dots are the DHU stem, whereas the third and fourth are the anticodon stem. The anticodon is given, along with the start or end of an adjacent downstream gene where they fall within the region shown. The arrow associated with the downstream gene shows the coding direction. Where the arrow is to the left, it indicates the end of that gene.

FIG. 3.—

Examples of inferred tRNA secondary structure from each cecidomyiid genome. Note consistent lack of a TΨC arm across genera; the overlap of the tRNA^Pro gene with tRNA^Thr on opposing strands in Asphondylia; the overlap of tRNA^Trp with the cox1 gene in Asphondylia; and tRNA^Tyr shown here in Mayetiola is found in a different genomic positions in each genus, between nad2 and cox1 in Rhopalomyia, between nad3 and nad5 in Mayetiola, and between cytb and nad1 in Asphondylia.

FIG. 4.—

Phylogeny of cecidomyiid genera and outgroup based on sequence data from cytochrome oxidase subunit I gene. Numbers above branches are MP bootstrap, ML bootstrap, and Bayesian posterior probabilities. Taxa displaying incomplete inferred secondary tRNA structure are denoted at the tips.