Complete mitochondrial genome of the diving beetle, Cybister brevis Aubé, 1838 (Coleoptera, Dytiscidae) from Jeju Island.

The mitochondrial genome of Cybister brevis Aubé, 1838, is 16,198 bp long and includes 37 genes that are highly conserved in the family Dytiscidae. Phylogenetic analysis revealed that all genera in Dytiscidae, except Hydroporus and Oreodytes, are monophyletic. The Hydroporini tribe was found to be polyphyletic and closely associated with the Hygrotini, Bidessini, and Hyphydrini tribes. Dytiscinae was found to be a highly divergent polyphyletic group comprising three distinct clades. This study also revealed that C. brevis is closely related to Cybister japonicus and that the tribe Cybistrini diverged relatively early compared to other tribes in Hydroporinae. These findings are consistent with those of previous studies and provide new insights into the phylogeny of the Dytiscidae family, which has previously shown discrepancies between morphological characteristics and molecular data. The genome-level analyses conducted in this study serve as a valuable foundation for future investigations into the Dysticidae evolutionary history.

Subspecific Synonym of Monochamus alternatus (Coleoptera: Cerambycidae): Population Genetics and Morphological Reassessment.

Monochamus alternatus Hope, 1842, is a major forest pest that hosts the pathogenic pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner and Buhrer, 1934) Nickle 1970. Taxonomically, M. alternatus is currently divided into two subspecies, based on morphology and geography: Monochamus alternatus alternatus Hope, 1842 in China, Taiwan, Tibet, Vietnam, and Laos and Monochamus alternatus endai Makihara, 2004 in South Korea and Japan. Despite their economic importance, the subspecies taxonomy of M. alternatus has never been tested after the first description. In this study, we aimed to reassess the subspecies taxonomy of M. alternatus using molecular and morphological data. For morphological analysis, we examined three major morphological characters (pronotal longitudinal band, granulation on humeri, and elytral proximomedial spine) from 191 individuals from China, Korea, and Taiwan. Population genetic structures were examined using 85 de novo sequences and 82 public COI sequences from China, Korea, Japan, Malaysia, Taiwan, and a few intercepted specimens from the United States. All the genetic data were aligned as three different multiple sequence alignments. Individuals from each subspecies were morphologically and genetically scattered, not clustered according to subspecies in any of the analyses. Therefore, a new synonymy is proposed: Monochamus alternatus Hope, 1842 = Monochamus alternatus endai, syn. n. This study suggests a more robust classification of M. alternatus for the first time and ultimately will pose a substantial impact on implementing quarantine or forestry policies.

The mitochondrial genome of Stereolepis doederleini (Pempheriformes: Polyprionidae) and mitogenomic phylogeny of Pempheriformes.

The complete mitochondrial (mt) genome of Stereolepis doederleini was sequenced from a specimen collected in a commercial aquarium in Jeju Island. The sequence was 16,513 base pairs in length and, similar to other vertebrate mt genomes, included 37 mt genes and a noncoding control region; the gene order was identical to that of typical vertebrate mt genome. Mitochondrial genome sequences of 17 species from 12 families were used to reconstruct phylogenetic relationships within the order Pempheriformes. The phylogenetic trees were constructed with three methods (neighbor joining [NJ], maximum likelihood [ML], and Bayesian method) using 12 protein coding genes, but not ND6. In all phylogenetic trees, Pempheriformes were clustered into three strongly supported clades. Two Acropomatidae species (Synagrops japonicus in clade-Ⅰ and Doederleinia berycoides in clade-Ⅲ) were polyphyletic; S. japonicus was close to Lateolabracidae and was the sister of Glaucosomatidae + (Pempheridae/(Percophidae+Creediidae)), and D. berycoides was sister to Howellidae + Epigonidae. All phylogenetic trees supported a sister relationship between Creediidae and Percophidae in clade-Ⅰ. Glaucosomatidae formed a sister clade with Pempheridae. The relationships within clade-Ⅱ, which was composed of four families (Pentacerotidae, Polyprionidae, Banjosidae, and Bathyclupeidae), slightly differed between NJ/ML and BI tree topologies. In clade-Ⅲ, the relationships among Howellidae, Epigonidae, and Acropomatidae were strongly supported.

Lapathoside A Isolated from Fagopyrum esculentum Induces Apoptosis in Human Pancreatic Cancer Cells.

BACKGROUND/AIM: Lapathoside A, a phenylpropanoid ester, was isolated from the roots of buckwheat by searching for bioactive compounds against human pancreatic cancer cells. MATERIALS AND METHODS: Buckwheat root extracts, prepared by 70% ethanol, were separated into n-hexane, methylene chloride, ethyl acetate, n-butanol, and water fraction by solvent partitioning. Seven fractions were obtained from the ethyl acetate fraction by liquid chromatography, and fraction No. 6 contained lapathoside A. The effects of lapathoside A on Panc-1 and SNU-213 human pancreatic cancer cell lines were examined. RESULTS: The structure of lapathoside A was determined by liquid chromatography-mass spectrometry, liquid chromatography-tandem mass spectrometry, and nuclear magnetic resonance analysis. Next, we investigated whether lapathoside A has anticancer activity in human pancreatic cancer cell lines (PANC-1 and SNU-213). After treatment with 25 µM lapathoside A, viability of PANC-1 and SNU-213 cells decreased to about 40 and 27%, respectively. In addition, lapathoside A treatment also increased apoptosis while affecting the expression levels of apoptotic proteins. CONCLUSION: The effect of lapathoside A on apoptosis was confirmed in pancreatic cancer cell lines, supporting the application of lapathoside A in the treatment of pancreatic cancer.

The mitochondrial genome of the Jeju ground beetle Carabus smaragdinus monilifer (Coleoptera, Carabidae).

The complete mitochondrial genome of the Jeju ground beetle Carabus smaragdinus monilifer was analyzed to determine its structure, morphology, and other characteristics. The 16,737-bp long mitochondrial genome consisted of 37 genes, including 13 protein-coding genes, two rRNAs, and 22 tRNAs. The order, encoding direction, and the initiation and termination codons of the 37 genes of C. smaragdinus monilifer were identical to those of other species in the family Carabidae. Phylogenetic analysis revealed that C. smaragdinus monilifer is clustered with Carabus lafossei. Herein, we have provided the complete mitochondrial genome sequence of C. smaragdinus monilifer to understand the phylogeny of Carabidae.

Complete mitochondrial genome of the Ussuri white-toothed shrew Crocidura lasiura (Insectivora, Soricidae).

We obtained the complete mitochondrial genome of the Ussuri white-toothed shrew Crocidura lasiura (Insectivora, Soricidae) at 17 362 base pairs (bp) containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. Its gene order is identical to that of other vertebrates. Several repeat elements were identified in the non-coding control region (D-loop). Phylogenetic tree using mt protein-coding gene sequences showed that C. lasiura was closely related to C. attenuata. The reports of mt genome sequences of Crocidura were not enough to study phylogenetic relationships in genome levels. However, this report may help us to understand the phylogenetic relationships and evolutionary history of Crocidura.

Complete mitochondrial genome of the far eastern Myotis, Myotis bombinus (Chiroptera, Vespertilionidae).

The complete mitochondrial genome of the Far Eastern Myotis, Myotis bombinus (Chiroptera, Vespertilionidae) is determined in this study. It is 17 128 base pairs in length with 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. Its gene order is identical to that of other typical vertebrates. There are two tandem repeat sequences in the non-coding control region. Each repeat sequences contains 5 copies of 81 nucleotides and 42 copies of 6 nucleotides. Phylogenetic tree of mt 13 protein-coding gene sequences of 18 species in the family Vespertilionidae shows two distinct clades. Clade I consists of Myotis and Murina, while Clade II contains all other species analyzed.

Mitochondrial genome sequence of Sibynophis chinensis (Squamata, Colubridae).

The complete mitochondrial (mt) genome of the Chinese many-toothed snake, Sibynophis chinensis, was sequenced and found to be 17,163 bp in length. The arrangement of 13 protein-coding genes, tRNAs and rRNAs was identical to that of other common snake mt genomes. The mt protein-coding genes of S. chinensis utilized ATA, ATG, ATA and GTG as initiation codons and AGA, AGG, TAA, TAG and T as termination codons. Among three tRNA clusters (LQM, WANCY and HSL), LQM was found instead of IQM, which is common in other vertebrates. We also identified two control regions that contained several conserved elements known as conserved sequence blocks and termination-associated sequences related to mt replication and transcription.

Migration route estimation of the Jeju striped field mouse Apodemus agrarius chejuensis (Rodentia, Muridae).

The taxonomic relationship between two Korean field mice species, Apodemus agrarius coreae and A. a. chejuensis, as well as their possible historic migration routes, was examined by molecular genetic analysis of the complete mitochondrial cytochrome b gene of 73 mice collected from the Korean Peninsula and Jeju Island. Our findings suggest that A. a. coreae and A. a. chejuensis populations expanded and dispersed rapidly. Bayesian and network analysis showed that A. a. chejuensis is a clearly distinct population, and that A. a. chejuensis originated from the ancestral lineage of A. a. coreae. Based on our data, we hypothesize that the A. a. coreae population originated from eastern China or elsewhere. After the last glacial epoch, the lineage isolated from A. a. coreae had adapted to the new environment of Jeju Island, and with the reproductive isolation caused by the geographic barrier, this lineage eventually became a distinct population.

Complete mitochondrial genome of the longtooth grouper Epinephelus bruneus (Perciformes, Serranidae).

We determined the complete nucleotide sequence of the mitochondrial (mt) genome for the longtooth grouper, Epinephelus bruneus (Perciformes, Serranidae). This mt genome, consisting of 16,686 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region as those found in other vertebrates, with the gene order identical to that of typical vertebrates. A major noncoding region between the trnP and trnF genes (991 bp) was considered to be the control region (D-loop). Within this sequence, 22 copies of a 17-bp tandem repeat element, 5'-TGATATTACATATATGC-3', were identified in the control region unlike previous reported Epinephelus species.

Mitochondrial genome sequences of the striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis.

We determined the complete mitochondrial (mt) genome sequences of the striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis. The mt genomes of A. a. coreae and A. a. chejuensis are 16,260 and 16,261 base pairs in length, respectively. The general features of the 13 protein-coding genes of the two species are similar to those of other rodents. The TAG termination codon for NADH dehydrogenase subunit (ND) 3 is unique to Apodemus in the Muroidea. The L-strand replication origin has the potential to form a stable stem-loop structure. Within the control region, a termination-associated sequence and several conserved sequence blocks were observed. The diversity of the 13 protein-coding genes, 2 rRNAs, and 1 control region between the two species ranged between 0.005 (ATP8) and 0.027 (ND4L).

The mitochondrial genome of Apodemus peninsulae (Rodentia, Muridae).

The complete mitochondrial (mt) genome of the Korean field mouse Apodemus peninsulae was sequenced and found to be 16,266 bp in length. The mt protein-coding genes of A. peninsulae had ATG, GTG, ATC, and ATA as initiation codons and TAA, TAG, TA, and T as termination codons. Two forms each of trnL and trnS and the three tRNA clusters, IQM, WANCY, and HSL were identified, as in the typical Rodentia mt genome. Among tRNAs, abnormal cloverleaf structure of trnS((AGY)) was identified in DHU arm. The l-strand replication origin has the potential to form a stable stem-loop structure and control region has several conserved sequence elements.

Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations.

We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.

Comparison of the mitochondrial genomes of East Asian Pseudolabrus fishes.

We determined the complete mitochondrial genomes of Pseudolabrus sieboldi and P. eoethinus, and analyzed the genome organization, codon usage, and transition/transversion mutation ratio of the mitochondrial genome. The mitochondrial genomes of P. sieboldi and P. eoethinus are 16,507 and 16,508 bp in length, respectively, and consisted of 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs), which is typical for vertebrate mitochondrial DNA. All protein-coding genes of two species used the initiation codon ATG except the cytochrome c oxidase subunit (CO) 1, which began with GTG as an initiation codon. However, the termination codon for the NADH dehydrogenase subunit (ND) 6 gene encoded with TAA in P. sieboldi, and TAG in P. eoethinus. The 12S and 16S rRNA genes were 949 and 1694 bp, respectively, in P. sieboldi, and were 948 and 1693 bp in P. eoethinus. The A + T content of the two rRNA genes were 52.9% in P. sieboldi and 52.5% in P. eoethinus, which is slightly lower than that of other labrid species. The identity of the 13 protein-coding genes ranged between 67% (ND6) and 94% (CO2 and ATP8). The G + C contents of all of the protein-coding genes of P. sieboldi were slightly higher than those of P. eoethinus. Our data contribute to the identification, and further our understanding, of the comparative genetics of Pseudolabrus species distributed in East Asia.

Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae).

We determined the complete nucleotide sequence of the mitochondrial genome for the rabbitfish Siganus fuscescens (Perciformes, Siganidae). This mitochondrial genome, consisting of 16,491 base pairs (bp), included 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region similar those found in other vertebrates; the gene order was identical to that of typical vertebrates. Most of the genes of S. fuscescens were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. The reading frames of ATPase 8 and 6 and those of ND4L and ND4 overlapped by ten and seven nucleotides, respectively. All mitochondrial protein-coding genes began with an ATG start codon, except for CO1, which started with GTG. Open reading frames of S. fuscescens ended with TAA (ND1, CO1, ATPase 8, ND4L, ND5 and ND6), and the remainder had incomplete stop codons, either TA (ATPase 6 and CO3) or T (ND2, CO2, ND3, ND4, and Cytb). The origin of L-strand replication in S. fuscescens was located in a cluster of five tRNA genes (WANCY) and was 34 nucleotides in length. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (828 bp) was considered to be the control region (D-loop). Within this sequence, we identified a conserved sequence block characteristic of this region. The rabbitfish was grouped with Siganus canaliculatus in most parsimony analyses, which showed 100% bootstrap support for their divergence. These findings are useful for inferring phylogenetic relationships and identification within the suborder Acanthuroidei.

Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations.

We determined the complete nucleotide sequence of the mitochondrial genome for the rock bream, Oplegnathus fasciatus (Perciformes, Oplegnathidae). This mitochondrial genome, consisting of 16,511 base pairs (bp), encoded genes for 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a noncoding control region like those found in other vertebrates, with the gene order identical to that of typical vertebrates. Most of the genes of O. fasciatus were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pairs of genes overlapped: ATPase 8 and 6 and ND4L and ND4 by ten and seven nucleotides, respectively. The origin of L-strand replication in O. fasciatus was in a cluster of five tRNA genes (WANCY) and was 41 nucleotides in length. The conserved motif (5'-GCGGG-3') was found at the base of the stem within the tRNA-Cys gene. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (835 bp) was considered to be the control region (D-loop). Within this sequence, we identified a termination-associated sequence and a conserved sequence block characteristic to this region. In most parsimony analyses, the O. fasciatus was positioned in the clade including Emmelichthyidae, Lutjanidae, Percidae, Centrarchidae, and Sparidae, with 100% bootstrap support for their divergence.