Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea)

• Published in: Animals (Basel) 2023-06, Vol.13 (12), p.1985
• Main Authors: Huang, Yixin, Yang, Yuanhan, Qi, Liqing, Hu, Haoyuan, Rasplus, Jean-Yves, Wang, Xu
• Format: Article
• Language: English
• Subjects: ATP8 gene; Bats; Bayesian analysis; Biodiversity; Biological control; Biological evolution; Chalcidoidea; Evolutionary genetics; Gene order; Gene rearrangement; Genes; Genetic markers; Genetic testing; Genetics; Genomes; Genomics; Hypotheses; Life Sciences; Mitochondria; Mitochondrial DNA; mitogenome; Morphology; Nasonia vitripennis; Nucleotides; Pachycrepoideus vindemmiae; parasitic lifestyles; phylogenetic position; Phylogenetics; Phylogeny; Populations and Evolution; Positive selection; Proteins; Pteromalidae; Stop codon; Systematics, Phylogenetics and taxonomy; Taxonomy; Topology; Transfer RNA; Transposition; tRNA
• ISSN: 2076-2615; 2076-2615
• DOI: 10.3390/ani13121985

The mitochondrial genomes of , , , and were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for of , which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for , which lacks the DHU arm in all species. In , and lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the gene of was greater than 1, indicating putative positive selection. A novel transposition of in was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.