How are the mitochondrial genomes reorganized in Hexapoda? Differential evolution and the first report of convergences within Hexapoda

The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily

The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software. We found a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich-region and a D-loop. The L. coffeella mitochondrial gene organization is highly conserved with similarities to lepidopteran mitochondrial gene rearrangements (trnM-trnI-trnQ). We concatenated the 13 PCG to construct a phylogenetic tree and inferred the relationship between L. coffeella and other lepidopteran species. L. coffeella is found in the Lyonetiidae clade together with L. malifoliella and Lyonetia clerkella, both leaf miners. Interestingly, this clade is assigned in the Yponomeutoidea superfamily together with Gracillariidae, and both superfamilies displayed species with leaf-mining feeding habits.

Variability and evolution of gene order rearrangement in mitochondrial genomes of arthropods (except Hexapoda)

In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods.

Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny

Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.

Novel Gene Rearrangements in Mitochondrial Genomes of four families of Praying Mantises (Insecta, Mantodea) and Phylogenetic Relationships of Mantodea

The mitochondrial genome (mitogenome) plays an important role in phylogenetic studies of many species. The mitogenomes of many praying mantis groups have been well-studied, but mitogenomes of special mimic praying mantises, especially Acanthopoidea and Galinthiadoidea species, are still sorely lacking in the NCBI database. The present study analyzes five mitogenomes from four species of Acanthopoidea (Angela sp., Callibia diana, Coptopteryx sp., Raptrix fusca) and one of Galinthiadoidea (Galinthias amoena) that were sequenced by the primer-walking method. Among Angela sp. and Coptopteryx sp., three gene rearrangements were detected in ND3-A-R-N-S-E-F and COX1-L2-COX2 gene regions, two of which were novel. In addition, individual tandem repeats were found in control regions of four mitogenomes (Angela sp., C. diana, Coptopteryx sp., G. amoena). For those, plausible explanations were derived from the tandem duplication-random loss (TDRL) model and the slipped-strand mispairing model. One potential motif was found in Acanthopidae that was seen as a synapomorphy. Several conserved block sequences (CBSs) were detected within Acanthopoidea that paved the way for the design of specific primers. Via BI and ML analysis, based on four datasets (PCG12, PCG12R, PCG123, PCG123R), the merged phylogenetic tree within Mantodea was reconstructed. This showed that the monophyly of Acanthopoidea was supported and that the PCG12R dataset was the most suitable for reconstructing the phylogenetic tree within Mantodea.

Complete mitochondrial genome of Phoneutria depilata (Araneae, Ctenidae): New Insights into the Phylogeny and Evolution of Spiders

Spiders (Araneae) are the most abundant terrestrial predators and megadiverse on earth. In recent years, the mitochondrial genome of a great diversity of species has been sequenced, mainly for ecological and commercial purposes. These studies have uncovered the existence of a variety of mitochondrial genome rearrangements. However, there is poor genetic information in several taxonomic families of spiders. We have sequenced the complete genome of Phoneutria depilata (Ctenidae) and, based on this, extract the mitogenomes of other ctenid species from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangements and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including eight Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogenetic and a gene order analysis from 76 spider mitochondrial genomes were carried out. Our results show a high rate of annotation error in the published spider mitochondrial genomes, which could lead to errors in phylogenetic inference. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.

Phylogenomic Analyses of the Tenthredinoidea Support the Familial Rank of Athaliidae (Insecta, Tenthredinoidea)

The systematic status of the genus Athalia and related genera is a perennial controversy in sawfly taxonomy. Several authors have hypothesized that the placement of Athalia within the Tenthredinidae is artificial, but no studies have focused on this topic. If the hypothesis that Athalia does not belong to Tenthredinidae can be supported, the taxonomic framework of Tenthredinoidea needs revision. We present a comprehensive phylogenomic study of Tenthredinoidae, focusing on the positions of Athalia and related genera by sampling 80 representatives mainly of the Tenthredinoidea, including Heptamelinae and Blasticotomidae. Our phylogenetic reconstructions based on nuclear genes and mitochondrial (mt) sequences support Athalia and related genera as a distinct clade sister to Tenthredinidae + (Cimbicidae + Diprionidae). A comparison of symphytan mitochondrial genomes reveals an innovative gene rearrangement pattern in Athaliidae, in which Dentathalia demonstrates a more ancestral pattern than Athalia and Hypsathalia. The lineage specificity of mt rRNA secondary structures also provides sufficient support to consider Athaliidae as a separate family. In summary, the phylogeny and genomic structural changes unanimously support the taxonomic treatment of Athaliidae as a family and the re-establishment of Dentathalia as a valid genus.

Mitogenomics of Chinch Bugs from China and Implications for Its Coevolutionary Relationship with Grasses

Blissidae (the Chinch bug) is a group with high species richness in Lygaeoidea, but there are only a few descriptions of mitochondrial genomes available. We obtained mitogenomes from 10 species of eight genera from Blissidae through second-generation sequencing technology. The length of the mitochondrial genome (excluding the control region) is between 14643 and 14385 bp; the content of AT is between 74.1% and 77.9%. The sequence of the evolution rate of protein coding genes was as follows: ND5 > ATP8 > ND6 > ND2 > ND4 > ND4L > ND1 > ATP6 > ND3 > COIII > COII > CYTB > COI. The mitogenomic structure of Blissidae is highly conservative. Gene rearrangement is only found in Pirkimeru japonicus (PiGXBS1), which is formed as the duplication of tRNA-H. The intergenic spacer between ND4 and tRNA-H, which form an obvious stem-and-loop structure, was found in all samples in this study. The phylogenetic trees generated by BI and ML indicated that Blissidae can be divided into three major clades: Clade A (only included Macropes); Clade B ((Pirkimerus + Bochrus) + Iphicrates); and Clade C ((Ischnodemus + Capodemus) + (Cavelerius + Dimorphopterus)). The divergence within the Blissidae began at about 56 Ma. At the genus level, the divergence was concentrated at 30−51 Ma, slightly later than the diversification of Poaceae. The consistency of divergence time between Blissidae and Poaceae might hint at the coevolutionary relationship between them, but further molecular and biological evidence is still needed to prove it.

Comparative Mitogenome Analyses of Subgenera and Species Groups in Epeorus (Ephemeroptera: Heptageniidae)

Simple Summary

As one of the most species-rich genera of Ephemeroptera, Epeorus Eaton, 1881, was found to be widely distributed in Holarctic and Oriental regions, and nine subgenera have been reported. Previous phylogenetic studies of Epeorus were mainly focused on morphological characters or several gene fragments. Here, 15 mitogenomes of Epeorus are sequenced and the comparative mitogenome analysis of six subgenera is performed. The gene rearrangement of trnI-trnM-trnQ-NCR-ND2 was first found in the genus. In addition, differences in genetic composition and codon usage between the species with this kind of rearrangement and other Epeorus species were observed. Phylogenetic analyses show that three subgenera, Proepeorus, Belovius and Iron, are not monophyletic groups, and our results imply that gill structures are not always appropriate for the classification of subgenera in Epeorus.

Abstract

Epeorus Eaton, 1881 is a diverse mayfly genus in Heptageniidae comprising more than 100 species which are further divided into nine subgenera and several species groups. However, the classification and the phylogenetic relationships among them are still uncertain. Here, 15 complete mitochondrial genomes of Epeorus were sequenced and compared together with six available ones of same genus in the NCBI database. Based on morphological classification, the 21 mitogenomes were classified into six subgenera (Proepeorus, Epeorus s.str., Belovius, Iron, Caucasiron and Siniron) and four species groups (G1, G2, montanus and longimanus). Among all analyzed mitogenomes, the gene rearrangement of trnI-trnM-trnQ-NCR-ND2 was first found occurring in three species of group G1, whereas the gene block trnI-trnM-trnQ-trnM-ND2 was observed in all other mitogenomes of Epeorus. Furthermore, the genetic composition and codon usage of species in group G1 were also significantly different from all other Epeorus species, except group longimanus. The intergenic spacer between trnA and trnR, which has the stem-loop secondary structure, occurred in all 21 mitogenomes, and the sequences of stems and loops were conserved within species groups. Furthermore, the phylogenetic analyses strongly support the monophyly of all species groups, although three of six recognized subgenera Proepeorus, Belovius, and Iron, were shown as the non-monophyletic groups.

Mitochondrial phylogenomics and mitogenome organization in the parasitoid wasp family Braconidae (Hymenoptera: Ichneumonoidea)

Background

Mitochondrial (mt) nucleotide sequence data has been by far the most common tool employed to investigate evolutionary relationships. While often considered to be more useful for shallow evolutionary scales, mt genomes have been increasingly shown also to contain valuable phylogenetic information about deep relationships. Further, mt genome organization provides another important source of phylogenetic information and gene reorganizations which are known to be relatively frequent within the insect order Hymenoptera. Here we used a dense taxon sampling comprising 148 mt genomes (132 newly generated) collectively representing members of most of the currently recognised subfamilies of the parasitoid wasp family Braconidae, which is one of the largest radiations of hymenopterans. We employed this data to investigate the evolutionary relationships within the family and to assess the phylogenetic informativeness of previously known and newly discovered mt gene rearrangements.

Results

Most subfamilial relationships and their composition obtained were similar to those recovered in a previous phylogenomic study, such as the restoration of Trachypetinae and the recognition of Apozyginae and Proteropinae as valid braconid subfamilies. We confirmed and detected phylogenetic signal in previously known as well as novel mt gene rearrangements, including mt rearrangements within the cyclostome subfamilies Doryctinae and Rogadinae.

Conclusions

Our results showed that both the mt genome DNA sequence data and gene organization contain valuable phylogenetic signal to elucidate the evolution within Braconidae at different taxonomic levels. This study serves as a basis for further investigation of mt gene rearrangements at different taxonomic scales within the family.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01983-1.

Macrostructural Evolution of the Mitogenome of Butterflies (Lepidoptera, Papilionoidea)

Simple Summary

Papilionoidea is a superfamily of Lepidoptera encompassing about 19,000 species. In the present work, we study the evolution of the structure of the mitogenome of these lepidopterans. The mechanisms generating the eight arrangements known for Papilionoidea were investigated analysing the movements of different mitochondrial genes. Five newly sequenced/assembled mitogenomes were included in our analysis involving more than 600 genomes. We provide new findings that help to understand the evolution of the gene orders MIQGO, IMQGO, 2S1GO, ES1GO and S1NGO in different butterflies. We demonstrate that the evolution of the 2S1GO in Lycaenidae followed a complicated pathway with multiple events of duplication and loss of trnS1 and changes in anticodon. We describe two new gene orders 2FFGO and 4QGO for Ampittia subvittatus (Hesperiidae) and Bhutanitis thaidina (Papilionidae).

Abstract

The mitogenome of the species belonging to the Papilionodea (Lepidoptera) is a double stranded circular molecule containing the 37 genes shared by Metazoa. Eight mitochondrial gene orders are known in the Papilionoidea. MIQGO is the plesiomorphic gene order for this superfamily, while other mitochondrial arrangements have a very limited distribution. 2S1GO gene order is an exception and is present in several Lycaenidae and one species of Hesperiidae. We studied the macrostructural changes generating the gene orders of butterflies by analysing a large data set (611 taxa) containing 5 new mitochondrial sequences/assemblies and 87 de novo annotated mitogenomes. Our analysis supports a possible origin of the intergenic spacer trnQ-nad2, characterising MIQGO, from trnM. We showed that the homoplasious gene order IMQGO, shared by butterflies, species of ants, beetles and aphids, evolved through different transformational pathways. We identify a complicated evolutionary scenario for 2S1GO in Lycaenidae, characterised by multiple events of duplication/loss and change in anticodon of trnS1. We show that the gene orders ES1GO and S1NGO originated through a tandem duplication random loss mechanism. We describe two novel gene orders. Ampittia subvittatus (Hesperiidae) exhibits the gene order 2FFGO, characterised by two copies of trnF, one located in the canonical position and a second placed in the opposite strand between trnR and trnN. Bhutanitis thaidina (Papilionidae) exhibits the gene order 4QGO, characterised by the quadruplication of trnQ.

Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae.

First Report on Mitochondrial Gene Rearrangement in Non-Biting Midges, Revealing a Synapomorphy in Stenochironomus Kieffer (Diptera: Chironomidae)

Simple Summary

Gene rearrangement is an additional type of data to support relationships of taxa, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. The concept to use mitochondrial gene rearrangements as phylogenetic markers has been proposed since the mid-1980s, the synapomorphic gene rearrangements have been identified from many lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae). Here, seven new mitogenomes of the genus Stenochironomus were sequenced and analyzed. Coupled with published data, phylogenetic analyses were performed within Chironominae. The present study showed that mitogenomes of Stenochironomus are showing a higher A+T bias than other chironomid species. A synapomorphic gene rearrangement that the gene order rearranges from trnI-trnQ-trnM to trnI-trnM-trnQ was identified within Stenochironomus, which is the first instance of mitochondrial gene rearrangement discovered in the Chironomidae. The monophyly of the genus Stenochironomus was strongly supported by mitogenomes. Our study provides new insights into the mitochondrial gene order of Chironomidae, and provides a valuable resource for understanding synapomorphic gene rearrangements.

Abstract

(1) Background: Gene rearrangement of mitochondrial genome, especially those with phylogenetic signals, has long fascinated evolutionary biologists. The synapomorphic gene rearrangements have been identified across multiple orders and at many different taxonomic levels, supporting the monophyletic or systematic relationships of related lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae); (2) methods: in this study, the complete mitogenomes of seven Stenochironomus species were sequenced and analyzed for the first time; (3) results: each mitogenome of Stenochironomus contains 37 typical genes and a control region. The whole mitogenomes of Stenochironomus species exhibit a higher A+T bias than other published chironomid species. The gene order rearranges from trnI-trnQ-trnM to trnI-trnM-trnQ in all the seven mitogenomes of Stenochironomus, which might be act as a synapomorphy of the genus, supporting the monophyletic of Stenochironomus species. In addition, another derived gene cluster: trnA-trnG-ND3-trnR exists in Stenochironomus tobaduodecimus. The derived gene orders described above are the first case of mitochondrial gene rearrangement in Chironomidae. Coupled with published data, phylogenetic relationships were reconstructed within Chironominae, and strongly supported the monophyly of Stenochironomus; (4) conclusions: our study provides new insights into the mitochondrial gene order of Chironomidae, and provides a valuable resource for understanding the synapomorphic gene rearrangements.