We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between tRNASer (UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one tRNAArg-like sequence and one tRNALys-likes equence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.

The complete nucleotide sequences of the mitochondrial genome (mitogenome) from the white-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Cetoniidae) was determined. The 20,319-bp long circular genome is the longest among the completely sequenced arthropods. This extraordinary length of the genome stemmed from 5,654-bp long A+T-rich region composed of twenty-eight 117-bp tandem repeats, seven 82-bp tandem repeats, and each two 19-bp and 38-bp tandem repeats. The P. brevitarsis contains a typical gene complement, order, and arrangement identical to most common type found in insects. The P. brevitarsis COI gene does not have typical ATN codon. Thus, we also designated it as AAC (asparagine), which is found in the start context of all sequenced Polyphaga within Coleoptera. All tRNAs showed stable canonical clover-leaf structure of other mt tRNAs, except for tRNASer (AGN), DHU arm of which could not form stable stem-loop structure. The 5bp-long motif sequence (TAGTA) that has been suggested to be the possible binding site for the transcription termination peptide for the major-strand also was found betweent RNASer (UCN) and ND1, as have been detected in all sequenced coleopteran insects.

We analyzed a portion of mitochondrial COI gene sequences (658 bp) to investigate the genetic diversity and geographic variation of the swallowtail butterfly, Papilioxuthus L., and the cabbage butterfly, Pieris rapae (Lepidoptera: Papilionidae). P. xuthus showed a moderate level of sequence divergence (0.91% at maximum) in 15 haplotypes, whereas P. rapae showed a moderate to high level of sequence divergence (1.67% at maximum) in 30 haplotypes, compared with other relevant studies. Analyses of population genetic structure showed that most populations are not genetically differentiated in both species. The distribution pattern of both species appears to be consistent with category IV of the phylogeographic pattern sensu Avise (Avise et al. 1987): a phylogenetic continuity, an absence of regional isolation of mtDNA clones, and extensive distribution of close clones. The observed pattern of genetic diversity and geographic variation of the two butterfly species seems to reflect the abundant habitats, abundant host plants, and flying abilities in connection with the lack of historical biogeographic barriers.

The 15,338-bp long complete mitochondrial genome (mitogenome) of the Japanese oak silkmoth, Antheraeayamamai (Lepidoptera: Saturniidae) was determined. This genome has a gene arrangement identical to those of all other sequenced lepidopteran insects, but differs from the most common type, as the result of the movement of tRNAMet to a position 5’-upstream of tRNAIle. No typical start codon of the A. yamamai COI gene is available. Instead, a tetranucleotide, TTAG, which is found at the beginning context of all sequenced lepidopteran insects was tentatively designated as the start codon for A. yamamai COI gene. Three of the 13 protein-coding genes (PCGs) harbor the incomplete termination codon, T or TA. All tRNAs formed stable stem-and-loop structures, with the exception of tRNASer(AGN), the DHU arm of which formed a simple loop as has been observed in many other metazoan mt tRNASer(AGN). The 334-bp long A+T-rich region is noteworthy in that it harbors tRNA-likestructures, as has also been seen in the A+T-rich regions of other insect mitogenomes. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As has been previously suggested, Bombycidae (Bombyxmori and B.mandarina) and Saturniidae (A.yamamai and Caligula boisduvalii) formed a reciprocal monophyletic group.

We determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae) that is an endangered insect species in Korea. The genome was sequenced from four overlapping fragments: two short fragments and two long fragments. The 15,857-bp long P. hilaris mitochondrial genome has the gene content typical of animal mitochondrial genome: 13 protein-coding genes, 22 tRNA genes, 2 ribosomal genes, and one non-coding A+T-rich region. The gene arrangement of the molecule is identical to the most common type found among insect mitochondrial gene arrangement that is regarded as ancestral for insects. Like several other coleopteran species the P. hilaris COI gene has typical mitochondrial start codon ATT. The 1,190-bp long A+T-rich region contains 57-bp long seven identical repeat sequences and at least seven stem-and-loop structures, composed of stems with perfect matches and loops with variable size. All P. hilaris tRNAs can be folded into the typical clover-leaf structure, with the exception of tRNASer(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. After more genomic and phylogenetic analyses are performed, further detailed information will be available.

In this study, we determined the complete mitochondrial genome of the jewel beetle, Chrysochroa fulgidissima (Coleoptera: Buprestidae), from four overlapping fragments. The 15,592-bp long C. fulgidissima mitogenome exhibits a gene arrangement and content identical to the most common type in insects. The start codon of the C. fulgidissima COI gene is unusual, in that no typical ATN codon is available. The 875-bp A+T-rich region is the shortest among the coleopteran mitogenomes that have thus far been sequenced in their entirety. The most unusual feature of the genome is the presence of three tRNA-like sequences within the A+T-rich region: two tRNALeu(UUR)-like sequences and one tRNAAsnlike sequence. These sequence stretches evidence the proper anticodon sequence and the potential to form secondary structures, but also harbor many mismatches in the stems. Phylogenetic analysis using a concatenation of 13 amino acid sequences of protein-coding genes among the available sequenced species of coleopteran superfamilies (Buprestoidea and Elateroidea belonging to the infraorder Elateriformnia, and Chrysomeloidea and Tenebrioroidea belonging to the infraorder Cucujoiformia) by Bayesian inference, maximum-parsimony analyses, and maximum-likelihood analysis unexpectedly revealed a lack of support for monophyletic Elateriformia.

We determined the complete mitochondrial genome (mitogenome) of the Japanese Oak Silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae) from two overlapping fragments and subsequent shotgun sequencing. The 15,601-bp long A. yamamai mitogenome contains gene arrangement and content identical to the most common arrangement found in lepidopteran insects. Most individual A. yamamai mitochondrial (mt) genes were well within the range found in the respective genes of other insects, except for small ribosomal RNA (1,037 bp). The 336-bp A+T-rich region is relatively smaller than that of other lepidopteran insects. The region is interesting in that it contains tRNA-like structures as found in the A+T-rich regions of other insect mitogenomes. The start codon of A. yamamai COI gene is unusual in that no typical one (ATN) is available. Three of the 13 protein-coding genes have incomplete termination codon T or TA. All tRNA formed stable stem-and-loop structure, except for tRNASer(AGN), the DHU arm of which formed a simple loop as seen in many other metazoan mt tRNASer(AGN).

We determined the complete mitogenome of the oriental mayfly, Ephemera orientalis (Ephemeroptera: Ephemeridae) and the dragonfly Davidius lunatus (Odonata: Gomphidae). The 16,463-bp long E. orientalis and the 15,912 bp long D. lunatus mitogenome contains gene arrangement and content identical to the most common type found in a diverse insect order. Most individual E. orientalis and D. lunatus mt genes were well within the size found in the respective genes of other insects. The initiation codon for the D. lunatus COI gene was typical as ATA, whereas no typical start codon was found in the start region of E. orientalis COI gene. The A+T-rich regions of both mitogenomes have a few unusual feature. The A+T-rich region of E. orientalis contains a tandem repeat composed of two identical copies of 55 bp long, whereas that of D. lunatus contains a tandem repeat composed of duplicated identical 261-bp copies and one partial copy of the repeat. Also, the A+T-rich region of E. orientalis contains a single sequence and that of D. lunatus contains nine sequences, along with the tandem triplicate sequences, that has the potential to form stem-and-loop structures, flanked by the conserved sequences, “TA(A)TA” at the 5’ end and “G(A)nT’ at the 3’ end. Furthermore, the A+T-rich region of D. lunatus contains two tRNA-like structures, tRNALeu(UUR)-like sequence and tRNATyr-like sequence that have proper anticodon TAA and clover-leaf structure that were previously found in the hymenopteran insects.

We determined the complete mitochondrial genome (mitogenome) of the jewel beetle, Chrysochroa fulgidissima (Coleoptera: Buprestidae) from two overlapping fragments and subsequent sub fragments. The 15,592-bp long C. fulgidissima mitogenome contains gene arrangement and content identical to the most common arrangement found in insects. Most individual C. fulgidissima mitochondrial (mt) genes were well within the range found in the respective genes of other insects. The 875-bp A+T-rich region is shortest among the coleopteran mitogenomes sequenced in their entirety. The region is interesting in that it contains several stem-and-loop structures and tRNA-like structure found in the A+T-rich regions of other insect mitogenomes. As seen in other insect motogenomes the start codon of C. fulgidissima COI gene also is unusual because no typical start codon is available. Three of the 13 protein-coding genes have incomplete termination codon T or TA. All tRNA formed stable stem-and-loop structure, except for tRNASer(AGN), the DHU arm of which formed a simple loop as seen in many other metazoan mt tRNASer(AGN).

The mason bee (Osmia cornifrons Radoszkowsky) is an excellent pollinator of apple. To understand geographic genetic variation of the species and relationships among populations sequenced a portion of mitochondrial COI gene, which corresponds to “DNA Barcode” region (658 bp) from 81 individuals collected over eight localities in Korea. The sequence data were used to investigate genetic diversity within populations and species, geographic variation within species, phylogeographic relationship among populations, and phylogenetic relationship among haplotypes. Summarized, overall moderate to low genetic diversity within populations and species was characteristic, concordant with the high potential to disperse of O. cornifrons in Korea. Although two populations were genetically subdivided from the remaining localities, no clear regional bias was observed. Overall, high rate of gene flow among localities and low FST was characteristic considering other relevant studies that investigated population genetic structure of other insects occurring in Korean peninsula.

The surveying of binding affinity between a particular transcription factor and DNA motifs is important in order to understand the developmental specific gene expression and regulatory networks of an organism. The microarray-based technologies (protein-binding microarrays; PBMs) provide useful predictions for understanding the transcriptional regulatory code in a genome-wide manner. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, named Q9-UPBM. Also, we developed rice promoter PBM (RPBM) using 19,480 rice promoter sequences containing 40 bp long probe with overlapping 20 bp (cover 1kb from 5’ upstream). We applied RISBZ1 protein, an endosperm specific basic leucine zipper transcription factor, to compare binding site specificities between Q9-UPBM and RPBM and find directly regulated promoter regions through the RPBM. Several cis-elements; Prolamin box (TGTAAAG), GCN4 motif (TGA(G/C)TCA), AACA motif (AACAAAA), and ACGT motif, are highly conserved in the promoters of cereal seed storage protein genes, and play a central role in controlling endosperm specific expression during seed maturation. Characterization of cis-elements and TFs has been performed on many storage protein genes of several crop plants, but the mechanisms are still poorly understood. Two chips provide RISBZ1 could bind to ACGT motif such as a CCACGTCA site and GGATGAC site as well as GCN4 motif known binding site. In RPBM binding affinity to CCACGTCA was highly significant, compared to GGATGAC site. The difference might be caused by the biased presence of specific promoter rather than Q9-UPBM. Also our results will provide direct insight into the importance of combinatorial interplay between cis-elements in regulating the expression of seed storage protein genes.