The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance

Abstract

Background Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance. Results The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness. Conclusions This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.

Complete mitochondrial genome analysis and molecular phylogenetic implications of Kennelia xylinana (Lepidoptera: Tortricidae)

“…In the present study, the problem associated with the phylogenetic relationships among Enarmoniini and three other tribes of Olethreutinae was evident. According to the BI tree, the phylogenetic relationships among the tribes in Olethreutinae can be inferred as: Enarmoniini + (Olethreutini + [Eucosmini + Grapholitini]), which is consistent with the results given by Yang et al (2021), whereas the ML tree showed that phylogenetic relationships are (Enarmoniini + Olethreutini) + (Eucosmini + Grapholitini). These two trees according to the analysis of nucleotide sequences are different from the findings of Regier et al (2012), where the tribes group as Olethreutini + (Enarmoniini + [Eucosmini + Grapholitini]).…”

“…The circumscription of tortricid tribes has been proposed primarily on the basis of adult morphology and larval biology (Horak & Brown, 1991; Horak, 1998, 2006; Kuznetsov & Stekolnikov, 1977, 1984; Powell, 1964; Razowski, 1976). The monophyly of most tribes is corroborated by molecular phylogeny; however, the relationship among the tribes in each subfamily has not been explicitly determined; the phylogenetic positions and compositions of several tribes have remained controversial, such as the taxonomic status of Polyorthini within Chlidanotinae; that of Cochylini and Epitymbiini within Tortricinae; that of Gatesclarkeanini, Endotheniini, and Bactrini within Olethreutinae; the phylogenetic positions of Phricanthini and Schoenotenini within Tortricinae; and the monophyly of Olethreutini within Olethreutinae (Fagua et al, 2016; Horak 2006; Regier et al, 2012; Safonkin, 2007; Yang et al, 2021). To understand the evolution of Tortricidae, further research involving a wide range of taxa is needed.…”

The mitochondrial genomes of the Geometroidea (Lepidoptera) and their phylogenetic implications

“…In addition, the tree based on PCGAA dataset showed a similar topology with that of PCG12R and PCG12 datasets. These results overall indicate that the third coding positions of 13 PCGs contain high phylogenetic informativeness although they may have experienced some substitution saturation (Yang et al, 2021 ). Regardless of the Pseudobistonidae with no mitogenome available, the close relationship between Epicopeiidae and Sematuridae is recovered by multilocus data in previous molecular studies (Rajaei et al, 2015 ; Wang et al, 2019 ).…”

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

“…As a result, they integrated gene sequences into a “supermatrix” to boost phylogenetic signal and node support. However, simultaneous analysis of linked gene sequences should be treated with caution, as biases can interfere with phylogenetic inferences due to strongly supportive clades erroneously grouped based on multiple substitution artifacts (e.g., heterogeneity of nucleotide composition [ 259 , 260 ], change in speed at different sites [ 261 , 262 ] and an increase in the sample of taxa [ 254 , 255 , 263 , 264 ].…”