Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans

Abstract

The Symphyta is traditionally accepted as a paraphyletic group located in a basal position of the order Hymenoptera. Herein, we conducted a comparative analysis of the mitochondrial genomes in the Symphyta by describing two newly sequenced ones, from Trichiosoma anthracinum, representing the first mitochondrial genome in family Cimbicidae, and Asiemphytus rufocephalus, from family Tenthredinidae. The sequenced lengths of these two mitochondrial genomes were 15,392 and 14,864 bp, respectively. Within the sequenced region, trnC and trnY were rearranged to the upstream of trnI-nad2 in T. anthracinum, while in A. rufocephalus all sequenced genes were arranged in the putative insect ancestral gene arrangement. Rearrangement of the tRNA genes is common in the Symphyta. The rearranged genes are mainly from trnL1 and two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY. The mitochondrial genomes of Symphyta show a biased usage of A and T rather than G and C. Protein-coding genes in Symphyta species show a lower evolutionary rate than those of Apocrita. The Ka/Ks ratios were all less than 1, indicating purifying selection of Symphyta species. Phylogenetic analyses supported the paraphyly and basal position of Symphyta in Hymenoptera. The well-supported phylogenetic relationship in the study is Tenthredinoidea + (Cephoidea + (Orussoidea + Apocrita)).

Figure 1. Mitochondrial genome organization of Symphyta referenced with the ancestral insect mitochondrial genomes.

Genes are transcribed from left to right except for those indicated by a line. PCGs, rRNA, and A+T-rich region genes are marked in yellow, pink, and white, respectively, while tRNA genes are marked in green and designated by the single-letter amino acid code.

Figure 2. Three-dimensional scatter-plot of the AT- and GC-skew and A+T% of the mitochondrial genomes of Symphyta.

Species of Tenthredinoidea are represented by red dots, Cephoidea by green dots, Orussoidea by blue dots, and Apocrita by yellow dots. al: Allantus luctifer; ar: Asiemphytus rufocephalus; mp: Monocellicampa pruni; tt: Tenthredo tienmushana; ta: Trichiosoma anthracinum; pc: Perga condei; cc: Cephus cinctus; cp: Cephus pygmeus; cs: Cephus sareptanus; oo: Orussus occidentalis; am: Apis mellifera; vb: Vespa bicolor; ds: Diadegma semiclausum; ve: Vanhornia eucnemidarum.

Figure 3. Relative synonymous codon usage (RSCU) of the mitochondrial genomes of Symphyta.

The stop codon is not given.

Figure 4. Evolutionary rates of Symphyta mitochondrial genomes.

The number of nonsynonymous substitutions per nonsynonymous site (Ka), the number of synonymous substitutions per synonymous site (Ks), and the ratio of Ka/Ks for each Symphyta mitochondrial genome are given, using that of A. appendiculatus as a reference sequence.

Figure 5. Scatter-plot graphics performed to test the saturation of the nucleotide substitution in the mitochondrial genomes in Symphyta.

Pairwise distances were calculated for the 12 partitions, the first, second and third codon positions of the 13 PCGs and all the partitions’ concatenated matrix.

Figure 6. Phylogenetic relationships of the Symphyta inferred from nucleotide sequences of the mitochondrial genome using three matrices (P123, P123R and P12T), referring to the Bayesian/Maximum Likelihood methods.

The numbers separated by “/” indicate the posterior probability and bootstrap values of the corresponding nodes (P123 using BI/P123R using BI/P12T using BI/P123 using ML/P123R using ML/P12T using ML). “*” indicates that the node was fully supported by all six inferences.