First report of the complete mitogenome of Microchironomus tabarui Sasa, 1987 (Diptera, Chironomidae) from Hebei Province, China

Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae)

(1) Background: Mitochondrial genomes have been extensively employed as a crucial marker in numerous dipteran families for understanding phylogenetics and systematics relations, thereby playing a pivotal role in molecular biology studies. The phylogenetic relationship of the Harnischia generic complex remains contentious due to the paucity of taxonomic and molecular data. Specifically, the evolutionary relationships among Cryptochironomus, Demicryptochironomus, and Harnischia are still unclear. (2) Methods: In this study, Polypedilum and Endochironomus were used as outgroups to analyze phylogenetic relationships among Cryptochironomus, Demicryptochironomus, and Harnischia, mitogenomes of four Cryptochironomus, two Demicryptochironomus, two Harnischia, and two Cladopelma were newly sequenced. Subsequently, we conducted a thorough analysis of the nucleotide composition, sequence length, and evolutionary rate. (3) Results: All mitogenomes exhibited structural conservation, with all genes consistently arranged in the identical order as that of the ancestral mitogenome. Nucleotide composition varied significantly among different genes, and the control region displayed the highest A + T content. All protein-coding genes undergo rigorous purification selection, with the ATP8 gene exhibiting the most rapid evolutionary rate among them. Utilizing Bayesian Inference (BI) and Maximum Likelihood (ML) methods across various databases, we reconstructed the phylogenetic relationships among the genera within the Harnischia generic complex, drawing insights from an analysis of 14 mitochondrial genomes. (4) Conclusions: Our results showed that the monophyly of the genera Harnischia was well supported in all topologies; Cryptochironomus is sister to Demicryptochironomus.

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.

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.

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.

First report of the complete mitogenome of Tanypus punctipennis Meigen, 1818 (Diptera, Chironomidae) from Hebei Province, China

Tanypus punctipennis Meigen, 1818 is an important bioindicator for freshwater ecosystems monitoring. Although COI barcode analyses have been performed on T. punctipennis, the mitogenome of this taxon has not been assembled and analyzed. Here, the complete mitogenome of T. punctipennis was sequenced and analyzed to confirm the systematic and phylogenetic history of this species. The mitogenome is 16,215 bp long with high A + T content, and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a noncoding control region. The phylogenomic analysis supports monophyletic Tanypodinae and close relationship between T. punctipennis and Clinotanypus. Our results indicate that mitogenomes showed strong signals in phylogenetic reconstructions at the genus level of Tanypodinae.

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.