Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny.

Boying Zheng,Jingxian Liu,Ruizhong Yuan,Cornelis Van Achterberg,Pu Tang,Xuexin Chen,Yuanyuan Han

doi:10.3390/insects13020124

Boying Zheng, Jingxian Liu + Show 5 more

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https://doi.org/10.3390/insects13020124

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Abstract

Simple SummaryNearly a hundred mitochondrial genomes of ichneumonid wasps are newly reported. Comparative mitogenomics of 104 mitochondrial genomes representing 33 subfamilies of Ichneumonidae, as well as its implications for phylogeny, were studied. We found that the mitochondrial genomes of ichneumonid wasps were highly conserved in their base composition and had low evolutionary rates, but were diverse in gene order. There are 38 types of gene rearrangement events in 104 ichneumonid mitochondrial genomes, of which 30 novel rearrangement types (R3-6, R8-R10, R12-R15, R17-R18, R20-R35 and R38) and a hot spot rearrangement around R1, with a shuffled tRNA cluster trnW-trnY-trnC and trnI-trnQ-trnM, were detected. The relationships among these subfamilies are firstly discussed based on mitochondrial genomes at a large scale. We suggest five subfamily groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively.Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.

Highlights

The family Ichneumonidae (Insecta: Hymenoptera) is one of the most species-rich families of insects, with approximately 25,000 described species, and many more are likely to be found [1,2,3]
Most tRNA genes are contained in our sequences, and the details are described in the gene rearrangement section
Because the base composition bias was found in protein-coding gene (PCGs) sequences, we considered that the reversal in Braconidae was caused by codon usage bias rather than the common GC

Summary

Introduction

The family Ichneumonidae (Insecta: Hymenoptera) is one of the most species-rich families of insects, with approximately 25,000 described species, and many more are likely to be found [1,2,3]. Ichneumonidae, or Darwin wasps, have a mega-diversity of specialized morphological and biological characteristics, and a world-wide distribution [4]. They parasitize holometabolous insects and occasionally spiders, and their types of life history are diversified, including ecto- and endoparasitoism and idiobiont/koinobiont strategies [5,6]. The earliest high-level groupings of Ichneumonidae were proposed based on larval morphology. Ichneumoniformes [7,8], Ophioniformes [9] and Pimpliformes [10] were recognized as the main high-level groupings of Ichneumonidae. Most studies focus on the sequence of a single gene (usually 28S rRNA) or combined morphological and biological characteristics to explore subfamily relationships. Quicke et al [2,11,12]

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