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

Mitogenomic analysis and phylogenetic relationships of Agrilinae: Insights into the evolutionary patterns of a diverse buprestid subfamily

Agrilinae is the largest subfamily in Buprestidae, which includes the four tribes, namely Coraebini, Agrilini, Aphanisticini, and Tracheini. However, there is a need to verify the evolutionary relationships among the taxa in Buprestidae. Thus, to explore the phylogenetic position of Aphanisticini, the mitochondrial genomes of Endelus continentalis and Cantonius szechuanensis were sequenced using next-generation sequencing technology. Three other mitogenomes of agriline beetles, Agrilus discalis, Sambus kanssuensis, and Habroloma sp., were also sequenced for the phylogenetic analyses. The divergence time of Buprestidae was estimated based on the mitogenomes. The general features of the known mitogenomes of Agrilinae were compared, analyzed, and summarized. Out of these five species, S. kanssuensis had the shortest mitogenome length (15,411), while Habroloma sp. had the longest (16,273). The gene arrangement of the five new sequences was identical to that of the reported buprestid mitogenomes. The Ka/Ks ratios of Meliboeus (0.79) and Endelus (0.78) were significantly larger than those of the other agriline genera. The results of the phylogeny indicated that Aphanisticini was more closely related to Tracheini and that the genus Sambus separated from the base of the Agrilinae clade at about 130 Ma. Moreover, Aphanisticini and Tracheini diverged at around 26 Ma.

Comparative mitogenomes reveal diverse and novel gene rearrangements in the genus Meteorus (Hymenoptera: Braconidae)

Meteorus Haliday, 1835 is a cosmopolitan genus within Braconidae (Hymenoptera). They are koinobiont endoparasitoids of Coleoptera or Lepidoptera larvae. Only one mitogenome of this genus was available. Here, we sequenced and annotated three mitogenomes of Meteorus species, and found that the tRNA gene rearrangements in these mitogenomes were rich and diverse. Compared with the ancestral organization, only seven tRNAs (trnW, trnY, trnL2, trnH, trnT, trnP and trnV) were conserved and trnG had its own unique location in the four mitogenomes. This dramatic tRNA rearrangement was not observed in mitogenomes of other insect groups before. In addition, the tRNA cluster (trnA-trnR-trnN-trnS1-trnE-trnF) between nad3 and nad5 was rearranged into two patterns, i.e., trnE-trnA-trnR-trnN-trnS1 and trnA-trnR-trnS1-trnE-trnF-trnN. The phylogenetic results showed that the Meteorus species formed a clade within the subfamily Euphorinae, and were close to Zele (Hymenoptera, Braconidae, Euphorinae). In the Meteorus, two clades were reconstructed: M. sp. USNM and Meteorus pulchricornis forming one clade while the remaining two species forming another clade. This phylogenetic relationship also matched the tRNA rearrangement patterns. The diverse and phylogenetic signal of tRNA rearrangements within one genus provided insights into tRNA rearrangements of the mitochondrial genome at genus/species levels in insects.

First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications

Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.

Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications

The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.

Comparative analysis and phylogeny of mitochondrial genomes of Pentatomidae (Hemiptera: Pentatomoidea)

The Phyllocephalini is a group of herbivorous insects in Pentatomidae, which lack distinctive morphological characteristics and systematic studies. Up to now, there are only two complete mitochondrial genomes of Phyllocephalini have been reported. In this study, we sequenced and analyzed the complete mitochondrial genomes of three Phyllocephalini species, Gonopsis coccinea, Gonopsimorpha nigrosignata, and Chalcopis glandulosus, which were 16,534, 16,531, and 16,534 bp in length, respectively. The mitochondrial genomes contained 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region. The gene arrangement was consistent with that of the putative ancestral insect, with no rearrangement. The cox1 gene of Pentatomidae showed the lowest evolutionary rate among the protein-coding genes, the mean genetic distance of species, genera, and subfamilies of Pentatomidae increased hierarchically based on cox1 gene. The 16S rRNA of Pentatomidae was more conserved than 12S rRNA in sequence and secondary structure. All tRNAs could be folded into a typical cloverleaf structure except trnS1. The stem region was more conserved than the loop region in the secondary structure of tRNAs within Pentatomidae. Gonopsis coccinea and Gonopsimorpha nigrosignata had one type of tandem repetition unit in the control region, while C. glandulosus had two types. The heterogeneity analysis of Pentatomidae showed that Phyllocephalinae was the most heterogeneous. Phylogenetic trees based on the newly obtain mitochondrial genomes along with other 50 mitochondrial genomes of Pentatomidae using Bayesian Inference and Maximum Likelihood strongly supported the following three relationships: (((Anaxilaus + (Plautia + Glaucias)) + (Nezara + Palomena)) + (Eysarcorini + Carpocorini)), (Hoplistoderini + (Menidini + Asopinae)), and ((Sephelini + Halyini) + (Caystrini + (Cappaeini + (Placosternum + Phyllocephalini)))). The relationships within Phyllocephalini were (Chalcopis + (Dalsira + (Gonopsimorpha + Gonopsis))). Our results provide valuable molecular data for further phylogenetic analyses of Pentatomidae.

Mitogenomic Comparison of the Mole Crickets Gryllotalpidae with the Phylogenetic Implications (Orthoptera: Ensifera)

Owing to limited molecular data, the phylogenetic position of the family Gryllotalpidae is still controversial in the infraorder Gryllidea. Mitochondrial genome (mitogenome) plays a crucial role in reconstructing phylogenetic relationships and revealing the molecular evolution of insects. However, only four mitogenomes have been reported in Gryllotalpidae to date. Herein, we obtained the first mitogenomes of Gryllotalpa henana Cai & Niu, 1998 and the Chinese G. orientalis Burmeister, 1838, made a detailed comparison of all mitogenomes available in Gryllotalpidae and reconstructed the phylogeny of Gryllidea based on mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. The results show that the complete mitogenome sequences of G. henana (15,504 bp) and G. orientalis (15,497 bp) are conserved, both exhibiting the double-stranded circular structure, typical gene content and the ancestral insect gene arrangement. The complete mitogenome of G.henana exhibits the lowest average AT content ever detected in Gryllotalpidae, and even Gryllidea. The gene nad2 of both species has atypical initiation codon GTG. All tRNAs exhibit typical clover-leaf structure, except for trnS1 lacking the dihydrouridine (DHU) arm. A potential stem-loop structure, containing a (T)_n(TC)₂(T)_n sequence, is detected in the control region of all gryllotalpids investigated and is likely related to the replication initiation of the minority strand. The phylogenetic analyses recover the six families of Gryllidea as Gryllotalpidae + (Myrmecophilidae + (Mogoplistidae + (Trigonidiidae + (Phalangopsidae + Gryllidae)))), similar to the trees based on transcriptomic and mitogenomic data. However, the trees are slightly different from the multilocus phylogenies, which show the sister-group relationship of Gryllotalpidae and Myrmecophilidae. The contradictions between mitogenomic and multilocus trees are briefly discussed.