Mitochondrial genomes of three specimens of Gadus chalcogrammus Pallas 1,814 from Korea and Japan were completely analyzed by the primer walking method. They were 16,570~16,571 bp in length, each comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Their gene orders were identical to those of conspecific specimens, but exhibited unique haplotypes. In the phylogenetic tree, the juvenile Korean and adult Japanese specimens were separated from the dominant clade composed of specimens from Japan, Korea, the Bering Sea, and the Arctic, including the adult Korean specimen.

A previous studies depicting origin and sequence variability of the species using DNA barcoding region with the samples collected from Korea showed relatively low sequence variability. Thus, additional markers that reveal higher variability were necessitated to scrutinize population structure in connection with dispersal and invasive dynamics among international populations. Therefore, we sequenced two complete mitochondrial genomes (mitogenomes) of M. pruinosa from the two haplotypes occurring in Korea (H1 and H3). Comparison of the two mitogenomes each with 16,312 and 16,314 bp evidenced that one region located in the A+T-rich region to provide higher number of haplotypes (4 vs. 3), sequence divergence (1.636% vs. 0.636%), and variable sites (7 vs. 3) than those of DNA barcoding region from the screening test using 13 representative individuals. This variable region, in concatenation with the currently available DNA barcoding region might be useful for population genetic analysis of worldwide populations including those of Korea. †These authors contributed equally to this paper.

To verify the progenitor of B. mori, we sequenced 14 B. mori strains preserved in Korea and one B. mandarina collected in Korea and conducted phylogenetic analysis of Bombycidae using maximum-likelihood method and concatenated sequences of 13 PCGs and 2 rRNA genes. All B. mori strains, regardless of their origin, formed a strong monophyletic group, with the highest nodal support. This B. mori group was placed as the sister to the two B. mandarina collected each from Korea and Shandong, China with the highest nodal support. Finally, the remaining two B. mandarina, which were collected in Japan were independently placed as the most basal lineage of B. mori and B. mandarina group. These results appear to indicate that an immediate ancestor for the domestic silkworm strains may have been originated from China and Korea.

In this study, we sequenced two complete mitogenomes, belonging to the families Scythrididae (Scythris sinensis Felder & Rogenhofer, 1775) and Coleophoridae (Coleophora therinella Tengström, 1848) firstly in each family. Gelechioidea is one of the controversial lineages of Lepidoptera in its phylogenetic position and number of families. Phylogenetic analyses with concatenated sequences of the 13 PCGs and two RNA genes using the maximum likelihood method, placed Coleophoridae, represented only by C. therinella, as a sister group to the families Depressariidae and Autostichidae, with very low nodal support (7%). Scythrididae represented only by S. sinensis was placed as the sister to the family Stathmopodidae, with relatively high nodal support (86%). As more mitogenome sequences from the extended taxonomic groups are obtained further robust phylogenetic inference will be possible.

Nilaparvata lugens, brown planthoppers, is one of important pests on rice. Korean N. lugens is migrated from China and causing severe damages on rice in early September in Korea. For identifying biotypes of these N. lugens based on complete mitochondrial genomes, we completed mitochondrial genome of N. lugens captured in Hadong-gun, Gyoungsang-nam province in Korea. The circular mitogenome of N. lugens is 17,610 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 2,424 bp. The base composition was AT-biased (89.5%). 112 single nucleotide polymorphisms (SNPs) and 59 insertions and deletions are identified by comparing with Chinese N. lugens. Based on phylogenetic trees together with those of N. lugens captured in China, no clear phylogenetic relationship along with five biotypes, requiring more researches to achieve biotype identification including detailed analysis of sequence variations on mitochondrial genomes and whole genome analysis of N. lugens in near future.

Previous phylogenetic results often showed fluctuating positions of Geometroidea in Macroheterocera, particularly from mitochondrial genome (mitogenome)-based analyses. In this study, we sequenced mitogenomes of four geometrid moths to increase taxon diversity for the inference of phylogenetic positions of Geometroidea in Macroheterocera. The general genomic features found in Macroheterocera also were found in the four geometrid moths. Phylogenetic analyses using 71 representative mitogeneome sequences in Macroheterocera yielded the consensus superfamilial relationships (((((Bombycoidea + Lasiocampoidea) + Geometroidea) + Noctuoidea) + Drepanoidea) + Mimallonoidea), confirming the sister relationship of Geometroidea to (Bombycoidea + Lasiocampoidea) in both Bayesian Inference and Maximum-likelihood method.

We sequenced the complete mitochondrial genome (mitogenome) of Vespa velutina nigrithorax and V. ducalis (Hymenoptera: Vespidae). The genomes were 16,475-bp and 15,779-bp long and contained typical sets of genes. The V. velutina and V. ducalis A+T-rich region was 132-bp long and 166-bp long and was the shortest of all sequenced Vespoidea genomes. Start and stop codons in several Vespa species—including V. velutina and V. ducalis—were diversified, despite these species belonging to the same genus. In comparison with the ancestral mitogenomes, Vespa mitogenomes showed substantial gene rearrangement; however, we detected no gene rearrangement among Vespa species. We conducted phylogenetic reconstruction based on concatenated sequences of 13 PCGs and two rRNAs in available species of Vespoidea—22 species in six subfamilies in two families (Vespidae and Formicidae). The Bayesian inference and maximum likelihood (ML) methods revealed that each family formed strong monophyletic groups.

Currently, only limited number of mitochondrial genomes (mitogenome) is available from Odonata. In order to extend current mitogenome data for comparative biology and phylogeny we sequenced complete mitogenomes of two endangered dragonfly species, Libellula angelina and Nannophya pygmaea (Ododana: Libellulidae). The whole genomes were 15,233 bp in L. angelina and 15,112 bp in N. pygmaea and included a typical set of genes (13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and one major non-coding A+T-rich region. The arrangement of the genomes was identical to typical one found in insects. Phylogenetic reconstruction using concatenated sequences of 13 PCGs and two rRNAs of Odonata (17 species in eight families in three suborders) using both Bayesian Inference (BI) and Maximum Likelihood (ML) methods have shown a strong support for monophyletic Zygoptera (BI, BPP = 1 and ML, 100%). Currently, further scrutinized analysis is under progress.

Currently, phylogenetic relationships of Macroheterocera with the inclusion of Bombycoidea have been reconstructed using molecular data, but generated several hypotheses on familial relationships within Bombycoidea and among-superfamilial relationships within Macroheterocera. Thus, in this study, mitogenome-based superfamilial relationships of Macroheterocera and familial relationships among macroheteroceran superfamily, Bombycoidea, were tested with different algorithms and partition schemes. Additionally, two unrecorded species of Bombycoidea (Saturnia jonasii and Kentrochrysalis streckeri) detected in Korea using morphological and molecular data are presented.

The sister relationship between Trichoptera and Lepidoptera has often been supported in a diverse study, but mitochondrial genomes (mitogenomes) based lepidopteran phylogenetic studies have never utilized Trichoptera as outgroup mainly due to unavailability. Therefore, the effect of alternatives that were previously used (e.g., Diptera, Hymenoptera, and Orthoptera) or Trichoptera as outgroups on the lepidopteran phylogeny remained unknown. In this study, we sequenced three complete mitogenomes of Trichoptera belonging to two suborders and characterized the genomic features of Trichoptera and tested the outgroup effect for lepidopteran phylogeny. The 15,208 ~ 15,285-bp long caddisfly mitogenomes harbor gene content typical of the animal mitogenomes. The orientation and gene order of the three species belonging to the suborder Integripalpia was identical to that of the most common type that has been hypothesized as ancestral for insects, but Cheumatopsyche brevilineata belonging to another suborder Annulipalpia has rearranged QIM, all encoded in forward direction between the A+T-rich region and ND2, instead of the ancestral IQM, with Q inverted. Further, the annulipalpian species had a typical start codon ATG, instead of CGA that are commonly found in other trichopteran species and majority of Lepidoptera. Phylogenetic analysis with different outgroups (Diptera, Hymenoptera, and Orthoptera, Coleoptera, and Trichoptera) and 115 lepidopteran mitogenomes has shown insensitivity either with Trichoptera, Diptera, or Coleoptera, but artificial grouping and lowered nodal support were found with Hymenoptera. The Trichoptera-based consensus topology were: (((((((Bombycoidea + Noctuoidea) + Pyraloidea) + Papilionoidea) + Cossoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea).

We newly sequenced mitogenomes of five skippers belonging to Lepidoptera to obtain further insight into characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species in 19 families in eight superfamilies. The general genomic features found in the butterflies also were found in the five skippers: a high A/T composition (79.3% - 80.9%), dominant usage of TAA stop codon, similar skewness pattern in various levels, consistently long intergenic spacer sequence between tRNAGln - ND2 (64-87 bp), the ATACTAA motif betweent RNASer(UCN) and ND1, and characteristic features of the A+T-rich region (the motif ATAGA, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. Phylogenetic analyses mainly yielded the consensus superfamilial relationships ((((((Bombycoidea + Noctuoidea + Geometroidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea) with a high support for most nodes, confirming the validity of Macroheterocera and its sister relationship to Pyraloidea. Within Rhopalocera the familial relationships (Papilionidae + (Hesperiidae + (Pieridae + ((Lycaenidae + Riodinidae) + Nymphalidae))) were strongly supported, confirming invalidity of the superfamily Hesperioidea. On the other hand, superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships among Saturniidae, Sphingidae, and Bombycidae were dubious, requiring further representative taxon sampling.

Two complete mitochondrial genomes of the tobacco cutworm, Spodoptera litura (Lepidoptera: Noctuoidea) and the rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), were sequenced. Each 15,388 bp and 15,368 bp-long genome contained both the lepidopteran specific gene arrangement that differ from the most common arrangement of insects by the movement of tRNAMet to a position 5’-upstream of tRNAIle. Neither of the species have typical COI start codon. Instead, the CGA (arginine) sequence that is commonly present in other lepidopterans was also found both in S. litura and C. medinalis. The evolutionary rates among 13 protein-coding genes (PCGs) in Lepidoptera showed ATP8 the highest, whereas COI the lowest. The high A+T-content, which is characteristic of mitochondrial genome was well reflected in the two lepidopteran mitochondrial genomes: higher frequency of A/T-rich codons, severe A/T bias in 3rd codon position, and extremely high A/T content in the A+T-rich region. Because insect mitochondrial genomes harbor biased nucleotide and resultantly biased amino acid sequences, phylogenetic inference is often misled by them. Although each recoded and unrecoded datasets for nucleotide sequences and amino acid sequences of PCGs provided overall identical topology, regardless of recoded scheme, each nucleotide and amino acid dataset provided difference in the status of Macrolepidoptera, providing a monophyletic group by amino acid dataset, whereas non-monophyletic group by nucleotide dataset.

Two complete mitochondrial genomes (mitogenomes) of the endangered, lycaenid butterflies, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae), were sequenced. Each 15,349 bp and 15,248 bp-long genome contained both the lepidopteran specific gene arrangement that differ from the most common arrangement of insects by the movement of tRNAMet to a position 5’-upstream of tRNAIle. Neither of the species have typical COI start codon. Instead, the CGA (arginine) sequence that is commonly present in all other lepidopterans was also found in both lycaenids. The possible binding site for the transcription termination peptide, TACTA sequence, also was well retained in both species. The high A+T-content, which is a characteristic of insect mitogenomes was well reflected in the genomes in the form of higher frequency of codons with A/T nucleotides, severe A/T bias in 3rd codon position, and extremely high A/T content in the A+T-rich region. The 19 bp-long poly-T stretch and the downstream conserved motif ATAG, which were suggested previously to function as a structural signal for minor-strand mtDNA replication, was also well conserved in the A+T-rich region of both lycaenids. Phylogenetic analysis among lepidopteran superfamilies supported the relationships of either (((((Bombycoidea + Geometroidea) + Noctuoidea) + Papilionoidea) + Pyraloidea) + Tortricoidea) by concatenated amino acid sequence or (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) by concatenated nucleotide sequences of 1st and 2nd codon positions of 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, revealing fluctuating positions of Papilionoidea and Pyraloidea between the two data sets.