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

Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae)

The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.

New mitogenomes from the genus Cricotopus (Diptera: Chironomidae, Orthocladiinae): Characterization and phylogenetic implications

Cricotopus is a large and diverse genus of non-biting midges composed of several subgenera. Complete mitogenome sequences are available for very few Cricotopus species. The subgenus Pseudocricotopus unites species with unusual morphological structures in adult male and pupal stages, however, molecular methods are needed to verify the placement of this subgenus within Cricotopus. We obtained mitogenomes of C. (Pseudocricotopus) cf. montanus and nine other Cricotopus species for phylogenetic analysis, coupled with two Rheocricotopus species and one Synorthocladius species as outgroups. The structure of the mitogenome was similar among these Cricotopus species, exhibiting A+T bias and retaining ancestral gene order. Mutation rate, estimated as Ka/Ks, varied among genes, and was highest for ATP8 and lowest for COI. The phylogenetic relationships among species of Cricotopus, Rheocricotopus and Synorthocladius was reconstructed using Bayesian inference and maximum likelihood estimation. The phylogenetic trees confirmed placement of subgenus Pseudocricotopus, represented by Cricotopus cf. montanus, within Cricotopus. Our study increases the library of chironomid mitogenomes and provides insight into the properties of their constituent genes.

New data on mitogenomes of Thienemanniella Kieffer, 1911 (Diptera: Chironomidae, Orthocladiinae)

The mitochondrial genome (mitogenome) has been widely used as a powerful marker in phylogenetic and evolutionary studies of various Dipteran groups. However, only a few mitogenomes from the Thienemanniella genus have been reported till now. Furthermore, there is still indeterminacy in the phylogenetic relationships of the genus Thienemanniella. In this study, mitogenomes of five Thienemanniella species were sequenced and analyzed newly. Combined with the published mitogenome of Thienemanniella nipponica, the obtained results showed that mitogenomes of Thienemanniella were conserved in structure, and all genes were observed to be arranged in the same gene order as the ancestral mitogenome. Nucleotide composition varied significantly among different genes, and the control region displayed the highest A + T content. All protein coding genes are subjected to purification selection, and the fastest evolving gene is ATP8. Maximum likelihood and Bayesian inference analyses showed the phylogeny of Thienemanniella which was supported in five topologies. Our present study provides valuable insight into the phylogenetic relationships of Thienemanniella species.

Complete mitochondrial genome of the non-biting midge Polypedilum henicurum Wang, 1995 (Diptera: Chironomidae)

The complete mitochondrial genome of Polypedilum henicurum was sequenced and analyzed. The whole mitogenome is 15,964 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The overall nucleotide composition is 39.5% A, 39.0% T, 13.1% C, and 8.4% G. Most PCGs start with ATN codon excluding COX1 (TTG) and all PCGs end with TAA codon. Gene arrangement stays the same with the ancestral mitochondrial genome. Bayesian inference phylogenetic tree supports its close relationship with P. unifascium. This work enriches the library of Chironomidae mitochondrial genomes and provides a valuable resource for understanding the evolutionary history of Polypedilum.

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.

New Mitogenomes of the Polypedilum Generic Complex (Diptera: Chironomidae): Characterization and Phylogenetic Implications

Mitochondrial genomics, as a useful marker for phylogenetics and systematics of organisms, are important for molecular biology studies. The phylogenetic relationships of the Polypedilum generic complex remains controversial, due to lack taxonomy and molecular information. In this study, we newly sequenced mitogenomes of 14 species of the Polypedilum generic complex. Coupled with three recently published sequences, we analyzed the nucleotide composition, sequence length, and evolutionary rate of this generic complex. The control region showed the highest AT content. The evolution rate of protein coding genes was as follows: ATP8 > ND6 > ND5 > ND3 > ND2 > ND4L > ND4 > COX1 > ND1 > CYTB > APT6 > COX2 > COX3. We reconstructed the phylogenetic relationships among the genera within the Polypedilum generic complex based on 19 mitochondrial genomes (seventeen ingroups and two outgroups), using Bayesian Inference (BI) and Maximum Likelihood (ML) methods for all databases. Phylogenetic analysis of 19 mitochondrial genomes demonstrated that the Endochironomus + Synendotendipes was sister to Phaenopsectra + Sergentia.

Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)

(1) Background: Chironomids are biological indicators, playing an important role in monitoring and assessing the changes in water ecosystems. Mitochondrial genomes have been widely applied as a molecular marker to analyze the taxonomy and phylogeny of insects. However, knowledge of the mitogenomes of Chironomus species is scarce at present, which limits our understanding of the evolutionary relationships among Chironomus. (2) Methods: In our study, the mitogenomes and their basic structure of 12 Chironomus species and one Microchironomus species were newly sequenced. Combined with reported mitogenomes, a total of 15 mitogenomes of Chironomus were selected for a comparative mitogenomic analysis and phylogenetic reconstruction of Chironomus. (3) Results: Each mitogenome of the Chironomus species has the typical 37 genes and a control region. The basic structure of the whole mitogenomes of Chironomus species is relatively conservative, and the genetic arrangements stay the same as the ancestral mitogenome. (4) Conclusions: Our study enriches the library of mitogenomes of chironomids and provides a valuable resource for understanding the evolutionary history of Chironomus.

New Mitogenome Features of Philopotamidae (Insecta: Trichoptera) with Two New Species of Gunungiella

A total of 14 individuals of Philopotamidae, from China, were examined. Six species in four genera, including two new species of the genus Gunungiella, were recognized. Their COI barcode sequences were extracted, mitogenomes were sequenced, assembled and analyzed. All of these sequences were used to further reveal the phylogenetic relationships of the family Philopotamidae. In addition, two new species: Gunungiella wangi n. sp., Gunungiella flabellata n. sp. were described and illustrated.

Characterization of Seventeen Complete Mitochondrial Genomes: Structural Features and Phylogenetic Implications of the Lepidopteran Insects

Lepidoptera (moths and butterflies) are widely distributed in the world, but high-level phylogeny in Lepidoptera remains uncertain. More mitochondrial genome (mitogenome) data can help to conduct comprehensive analysis and construct a robust phylogenetic tree. Here, we sequenced and annotated 17 complete moth mitogenomes and made comparative analysis with other moths. The gene order of trnM-trnI-trnQ in 17 moths was different from trnI-trnQ-trnM of ancestral insects. The number, type, and order of genes were consistent with reported moths. The length of newly sequenced complete mitogenomes ranged from 14,231 bp of Rhagastis albomarginatus to 15,756 bp of Numenes albofascia. These moth mitogenomes were typically with high A+T contents varied from 76.0% to 81.7% and exhibited negative GC skews. Among 13 protein coding genes (PCGs), some unusual initiations and terminations were found in part of newly sequenced moth mitogenomes. Three conserved gene-overlapping regions and one conserved intergenic region were detected among 17 mitogenomes. The phylogenetic relationship of major superfamilies in Macroheterocera was as follows: (Bombycoidea + Lasiocampoidea) + ((Drepanoidea + Geometroidea) + Noctuoidea)), which was different from previous studies. Moreover, the topology of Noctuoidea as (Notodontidae + (Erebidae + Noctuidae)) was supported by high Bayesian posterior probabilities (BPP = 1.0) and bootstrapping values (BSV = 100). This study greatly enriched the mitogenome database of moth and strengthened the high-level phylogenetic relationships of Lepidoptera.

First complete mitogenome of Axarus fungorum (Albu, 1980) from Guizhou Province, China (Diptera, Chironomidae)

Axarus fungorum (Albu, 1980) exhibits certain adaptations to different aquatic environments, appearing as an important evaluation element for freshwater quality monitoring. In this study, complete mitogenome of A. fungorum was provided for the first time to define the systematic and phylogenetic history of this taxon. The whole mitogenome is 15,696 bp long with high A + T content that consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a noncoding control region. ML analysis showed support for monophyly of Chironominae and close relationship between A. fungorum and Chironomus generic genera.

Mitogenomes provide new insights of evolutionary history of Boreheptagyiini and Diamesini (Diptera: Chironomidae: Diamesinae)

Mitogenomes have been widely used for phylogenetic reconstruction of various Dipteran groups, but specifically for chironomid, they have not been carried out to resolve the relationships. Diamesinae (Diptera: Chironomidae) are important bioindicators for freshwater ecosystem monitoring, but its evolutionary history remains uncertain for lack of information. Here, coupled with one previously published and 30 new mitogenomes of Diamesinae, we carried out comparative mitogenomic analysis and phylogenetic analysis. Mitogenomes of Diamesinae were conserved in structure, and all genes arranged in the same order as the ancestral insect mitogenome. All protein-coding genes in Diamesinae were under stronger purifying selection than those of other nonbiting midge species, which may exhibit signs of adaptation to life at cold living conditions. Phylogenetic analyses strongly supported the monophyly of Diamesinae, with Boreheptagyiini deeply nested within Diamesini. In addition, phylogenetic relationship of selected six genera was resolved, except Sympotthastia remained unstable. Our study revealed that the mitogenomes of Diamesinae are highly conserved, and they are practically useful for phylogenetic inference.