The complete mitochondrial genome of Pidorus atratus (Lepidoptera: Zygaenoidea: Zygaenidae)

Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae

BACKGROUND

The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops.

RESULTS

The mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae.

CONCLUSIONS

Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.

Complete mitochondrial genome of Parasa sinica: New insights into the phylogeny of Limacodidae

In this study, the whole mitochondrial genome (mitogenome) of Parasa sinica was sequenced. It contains 15,306 base pairs (bp), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding regulatory area (CR), all of which are shared by other lepidopterans. It follows the same gene order as ordinary lepidopterans. Further, out of these 37 genes, 23 are present on the heavy strand whereas the remaining 14 are located on the light strand. The A + T composition of the mitogenome is relatively high. Although P. sinica has a negative AT-skew and GC-skew, the GC-skew value is significantly lower than the AT-skew value. All PCGs, with the exception of CO1, carry the same start codon (ATN). All tRNAs exhibit the usual cloverleaf secondary structure. We identified the conserved motif "ATAGA + poly-T″ found in other lepidopteran insects at the beginning of the CR. We collected the concatenated PCGs sequences in the mitochondrial genome of 15 species of Zygaenoidea, with the sequences of Geometridae as outgroups, including P. sinica, and constructed phylogenetic trees using Bayesian inference (BI) and maximum likelihood (ML) methods. The monolineage of each superfamily is usually well supported. Based on phylogenetic analysis, P. sinica is a member of family Limacodidae, strongly supporting the monophyly of the Zygaenoidea groups.

Phylogenetic relationships of Limacodidae and insights into the higher phylogeny of Lepidoptera

To determine the systematic status of family Limacodidae within Lepidoptera, the complete mitochondrial genome (mitogenome) of Thosea sinensis (Lepidoptera: Zygaenoidea: Limacodidae) was sequenced. The genome is 15,544 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and an AT-rich region. These characteristics are similar to of other lepidopterans. The gene order of T. sinensis is identical to that of Ditrysia lepidopterans. The nucleotide composition of the T. sinensis mitochondrial genome is highly biased toward A + T nucleotides (81.1%) and exhibits negative AT and GC skew. All the other 13 PCGs except cox1 are initiated by ATN codons. All tRNA genes are folded into the typical cloverleaf secondary structure, except for trnS1, which lacked the dihydrouridine (DHU) stem. There are 20 intergenic spacer regions ranging from 1 to 56 bp in length, and two gene overlap regions throughout the entire genome. The AT-rich region includes the ATAGA motif, followed by a 19-bp poly T stretch, a microsatellite-like (AT)₁₀, and a poly-A element. Analysis of phylogenetic relationships indicated that T. sinensis belongs to the Limacodidae, and the monophyly of each lepidopteran family was well supported.

The complete mitochondrial genome of Amesia sanguiflua (Lepidoptera, Zygaenidae)

Amesia sanguiflua (Lepidoptera, Zygaenidae) is found in northern India, Myanmar, Indochina, Malay Peninsula, Sumatra, Java, and China. In the present study, we sequenced the complete mitochondrial genome of A. sanguiflua. The mitochondrial genome was 15,203 bp in length, containing a typical set of 37 genes (13 protein-coding genes, 2 rRNA genes, 22 tRNA genes) and a 346bp non-coding A+T-rich region. Phylogenetic analysis using mitochondrial genomes of 40 species showed that A. sanguiflua formed a well-supported monophyletic group with other Zygaenidae species.

The first mitochondrial genome for Phaudidae (Lepidoptera) with phylogenetic analyses of Zygaenoidea

Phauda flammans Walker belongs to Phaudidae (Lepidoptera), which is a holometabolous and leaf-eating pest that harms trees. So far, there is no mitochondrial (mt) genome reported of Phaudidae. Herein, we sequenced and annotated the complete mt genome of P. flammans representing the first mt genome of Phaudidae and predicted the secondary structures of its RNAs in this study. This mt genome is 15470 bp long consisting of 13 protein coding genes (PCGs), 22 tRNAs, 2 rRNAs and the control region, which are usually conserved in insects. Most PCGs used the standard ATN start codons and complete TAA/TAG termination codons. Almost all of tRNA genes exhibited cloverleaf secondary structures except that the dihydorouridine (DHU) arm of tRNA^Ser(AGN) was absent. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods all supported that Phaudidae was a single family being the sister group to Zygaenidae. More mt genomes are needed to better understand the phylogenetic relationships within Zygaenoidea in the future.