Massive gene rearrangements of mitochondrial genomes and implications for the phylogeny of Trichoptera (Insecta)

Abstract

Mitochondrial genomes have been widely used for phylogenetic reconstruction and evolutionary analysis in various groups of Insecta. Gene rearrangements in the mitogenome can be informative characters for phylogenetic reconstruction and adaptive evolution.Trichoptera is one of the most important groups of aquatic insects. Prior to this study, complete mitogenomes from Trichoptera were restricted to eight families, resulting in a biased view of their mitogenome structure and evolution. Here, we assemble new mitogenomes for 66 species by high-throughput sequencing. The mitogenomes of 19 families and 47 genera are documented for the first time. Combined with 16 previously published mitogenomes of Trichoptera, we find 14 kinds of gene rearrangement patterns novel for Trichoptera, including rearrangement of protein-coding genes, tRNAs and control regions. Simultaneously, we provide evidence for the occurrence of tandem duplication and non-random loss events in the mitogenomes of three families. Phylogenetic analyses show that Hydroptilidae was recovered as a sister group to Annulipalpia. The increased nucleotide substitution rate and adaptive evolution may have affected the mitochondrial gene rearrangements in Trichoptera. Our study offers new insights into the mechanisms and patterns of mitogenome rearrangements in Insecta at large and into the usefulness of mitogenomic gene order as a phylogenetic marker within Trichoptera.

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

“…ATP8 , ND6 , and ND5 showed higher ω value, indicating that they exhibited relatively relaxed purifying selection pressure. Meanwhile, COX2 and COX3 were under the hardly purifying selection, which were similar to previous research results regarding chironomids [ 2 , 3 , 10 , 43 ].…”

“…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 ).…”

“…Mitochondrial genomes are important molecular markers that have usually been used for studies on phylogeny, evolutionary history, speciation and phylogeography in insect groups [ 1 , 2 , 3 ], benefit by the maternal inheritance, high substitution, and easy availability [ 4 , 5 ]. Mitogenomes are known as the second genetic information system, because of its special genetic characteristics [ 6 ].…”

Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)

“…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].…”

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

“…Mitogenomes have been widely used in phylogenetics and population genetic studies, especially of insects (Cameron, 2014; Wang et al, 2021; Zhang et al, 2022; Zheng et al, 2018). The small size and ease of amplification of mitogenomes, their low degree of gene rearrangement and fast evolutionary rate make them ideal for molecular investigation of diversity and evolutionary relationships in aquatic insects (Chen & Du, 2015; Ge, Peng, et al, 2022; Ge, Zang, et al, 2022; Ma et al, 2022; Zheng et al, 2020). A dated phylogeny of Chironomidae at subfamily and lower taxonomic levels has been constructed (Cranston et al, 2012) using only four genes: two ribosomal, one nuclear and one mitochondrial gene.…”