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

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.

Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)

“…The ω value of each PCG was less than 1, showing that the non-synonymous substitution rate was less than the synonymous substitution rate, and indicating that 13 PCGs evolved under purifying selection pressure. ATP8 exhibited the highest ω value, while COI exhibited the lowest ω value, which was similar to other chironomids [8][9][10].…”

“…Mitogenomes are considered as useful molecular markers for phylogenetic and evolutionary analysis in many insect groups [2][3][4][5] Insects 2022, 13, 1164 2 of 11 due to their small genome size, maternal inheritance, low sequence recombination, and fast evolutionary rates [6,7]. With the wide application of the high-throughput sequencing technology, mitogenomes have proven successful in species delimitation and phylogenetics among aquatic insects [4,5,[8][9][10][11][12][13][14][15].…”

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

“…We compared the Ka/Ks value between Diamesinae and other subfamilies of Chironomidae. Previous studies reported the Ka/Ks values of mitochondrial PCGs of Orthocladiinae and Stenochironomus (Lin et al, 2022;Zheng et al, 2022), and the Ka/Ks values of each PCG in these chironomids are higher than that in Diamesinae (Table S3), indicating that the mitochondrial genomes of Diamesinae are under stronger purifying selection than other nonbiting midge species (Hurst, 2002). Mitochondrial genome played a central role in animal energy production, and stronger purification selection could enhance their conserved role in energy production (Hassanin et al, 2009;Yuan et al, 2020).…”

“…Benefiting from the advances of high‐throughput sequencing technology, an increasing number of complete mitogenomes have been sequenced among the Diptera (Kang et al, 2016 ; Li et al, 2020 ; Miao et al, 2020 ; Ramakodi et al, 2015 ; Tang, Yan, et al, 2019 ; Wang et al, 2021 ; Yan et al, 2021 ; Zhang et al, 2022 ), and have been widely used for mitochondrial structure comparison and phylogenetic analysis at different taxonomic levels (Chen et al, 2018 ; de Oliveira Aragão et al, 2019 ; Yan et al, 2019 ; Zhang et al, 2016 ; Zhang, Kang, et al, 2019 ). Prior to this study, rare mitogenomes of Chironomidae were available (Beckenbach, 2012 ; Deviatiiarov et al, 2017 ; Fang et al, 2022 ; Jiang et al, 2022 ; Kim et al, 2016 ; Kong et al, 2021 ; Lei et al, 2021 ; Park et al, 2020 ; Zhang, Xu, et al, 2019 ; Zheng et al, 2022 ; Zheng et al, 2021 ), limiting our understanding of their mitochondrial structure and phylogenetic pattern. Besides, it is still unknown whether mitogenomes can effectively resolve phylogenetic relationships at different levels within Chironomidae.…”

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

“…Their diversity of larval habitat, which includes wood-mining, and aquatic habit therein, also render them an important group for studying evolutionary biology [ 12 , 17 ]. Several taxonomy and molecular studies have examined the phylogenetic relationships of the Polypedilum generic complex [ 15 , 18 , 19 ], but uncertainties in classification schemes among these groups still persist [ 19 , 20 , 21 ].…”