Comparative Mitogenomic Analyses of Hydropsychidae Revealing the Novel Rearrangement of Protein-Coding Gene and tRNA (Trichoptera: Annulipalpia)

Abstract

Gene rearrangement of the mitochondrial genome of insects, especially the rearrangement of protein-coding genes, has long been a hot topic for entomologists. Although mitochondrial gene rearrangement is common within Annulipalpia, protein-coding gene rearrangement is relatively rare. As the largest family in Annulipalpia, the available mitogenomes from Hydropsychidae Curtis, 1835 are scarce, and thus restrict our interpretation of the mitogenome characteristic. In this study, we obtained 19 novel mitogenomes of Hydropsychidae, of which the mitogenomes of the genus Arctopsyche are published for the first time. Coupled with published hydropsychid mitogenome, we analyzed the nucleotide composition evolutionary rates and gene rearrangements of the mitogenomes among subfamilies. As a result, we found two novel gene rearrangement patterns within Hydropsychidae, including rearrangement of protein-coding genes. Meanwhile, our results consider that the protein-coding gene arrangement of Potamyia can be interpreted by the tandem duplication/random loss (TDRL) model. In addition, the phylogenetic relationships within Hydropsychidae constructed by two strategies (Bayesian inference and maximum likelihood) strongly support the monophyly of Arctopscychinae, Diplectroninae, Hydropsychinae, and Macronematinae. Our study provides new insights into the mechanisms and patterns of mitogenome rearrangements in Hydropsychidae.

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

“…The Ka/Ks value (ω) was usually used to measure the rate of sequence evolution by natural selection [ 45 , 46 ]. The result of Ka/Ks ratio of all 13 PCGs was less than one, ranging from 0.0958 ( COX3 ) to 0.7251 ( ATP8 ) ( Figure 3 ), which was same as other insects [ 43 , 44 ]. The evolution rate of 13 PCGs was as follows: ATP8 > ND6 > ND5 > ND3 > ND2 > ND4L > ND4 > COX1 > ND1 > CYTB > APT6 > COX2 > COX3 .…”

“…The nucleotide composition of the newly reported mitogenomes were similar ( Table 2 ), revealing the characteristic AT-biased composition in Chironomidae and other insects [ 2 , 3 , 10 , 25 , 42 , 43 , 44 ]. The AT content of the mitochondrial genomes ranged from 75.98% ( Stictochironomus akizukii ) to 79.94% ( Phaenopsectra flavipes ; Figure 2 ; Table 2 ).…”

Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)

“…The mitochondrial genome (mitogenome) of insects is a 14-20 kb circular molecule, including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding control region (CR) [1]. 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].…”

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

“…Although most PCGs terminated with the conventional TAA and TAG as stop codons, some of them have incomplete stop codons (T or TA) in some PCGs ( Supplementary Table S5 ). The start and stop codons were typical of insect mitogenomes ( Li et al, 2021 ; Ge et al, 2022 ). Relative synonymous codon usage (RSCU) values of three Meteorus species were analyzed ( Figure 2 ; Supplementary Table S6 ).…”

“…PCGs terminated with the conventional TAA and TAG as stop codons, some of them have incomplete stop codons (T or TA) in some PCGs (Supplementary Table S5). The start and stop codons were typical of insect mitogenomes (Li et al, 2021;Ge et al, 2022).…”