The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea.

BACKGROUND: Stomatopod crustaceans are aggressive marine predators featuring complex compound eyes and powerful raptorial appendages used for "smashing" or "spearing" prey and/or competitors. Among them, parasquilloids (superfamily Parasquilloidea) possess eyes with 2-3 midband rows of hexagonal ommatidia and spearing appendages. Here, we assembled and analyzed the complete mitochondrial genome of the parasquilloid Faughnia haani and explored family- and superfamily-level phylogenetic relationships within the Stomatopoda based on mitochondrial protein coding genes (PCGs). RESULTS: The mitochondrial genome of F. haani is 16,089 bp in length and encodes 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region that is relatively well organized, containing 2 GA-blocks, 4 poly-T stretches, various [TA(A)]n-blocks, and 2 hairpin structures. This organized control region is likely a synapomorphic characteristic in the Stomatopoda. Comparison of the control region among superfamilies shows that parasquilloid species are more similar to gonodactyloids than to squilloids and lysiosquilloids given the presence of various  poly-T stretches between the hairpin structures and [TA(A)]n-blocks. Synteny is identical to that reported for other stomatopods and corresponds to the Pancrustacea ground pattern. A maximum-likelihood phylogenetic tree based on PCGs revealed that Parasquilloidea is sister to Lysiosquilloidea and Gonodactyloidea and not to Squilloidea, contradicting previous phylogenetic studies. CONCLUSIONS: The novel phylogenetic position of Parasquilloidea revealed by our study indicates that 'spearing' raptorial appendages are plesiomorphic and that the 'smashing' type is either derived (as reported in previous studies) or apomorphic. Our results raise the possibility that the spearing raptorial claw may have independently evolved twice. The superfamily Parasquilloidea exhibits a closer relationship with other stomatopod superfamilies with a different raptorial claw type and with dissimilar numbers of midband rows of hexagonal ommatidia. Additional studies focusing on the assembly of mitochondrial genomes from species belonging to different genera, families, and superfamilies within the order Stomatopoda are warranted to reach a robust conclusion regarding the evolutionary history of this iconic clade based on mitochondrial PCGs.

Development of 17 polymorphic microsatellite loci from Jeju striped field mouse, Apodemus agrarius chejuensis (Rodentia: Muridae), by 454 pyrosequencing.

BACKGROUND: The striped field mouse, Apodemus agrarius, is the most common mammal in Korea. Although microsatellite loci for the species have been identified from populations in southwestern China, amplification of those markers for Korean populations have been unsuccessful. The complicated taxonomy of Korean striped field mouse including populations on Jeju Island (A. a chejuensis) necessitates identification of additional molecular markers. FINDINGS: We applied 454 pyrosequencing systems to develop a suite of microsatellite markers. Muscle tissue was harvested and sequenced from 30 Jeju striped field mouse specimens which yielded 12,165 reads with a mean length per read of 287 bp. From these reads, we identified 17 microsatellite loci for A. a. chejuensis and tested these new markers against samples of both A. a chejuensis and A. a coreae, the mainland taxon. All 17 loci were amplified successfully for both taxa. Of the total 17 loci, one locus failed to amplify for a population on Heuksan Island. The cross-species transferability was also tested with the allied taxon, A. peninsulae and confirmed successful for 12 loci. CONCLUSIONS: These newly developed markers will benefit studies of genetic structure, evolution, and resolving taxonomic problems of striped field mice and allied taxa in Korea.

Population Genetic Structure of the Malaria Vector Anopheles sinensis (Diptera: Culicidae) Sensu Stricto and Evidence for Possible Introgression in the Republic of Korea.

Anopheles sinensis Wiedemann sensu stricto (s.s.) is a dominant mosquito and considered a secondary malaria vector in the Republic of Korea (ROK). Despite the potential significance for malaria control, population genetics studies have been conducted using only mitochondrial DNA (mtDNA), and studies of the genetics of hybridization have never been attempted. In this study, 346 specimens from 23 localities were subject to experiments. Among them, 305 An. sinensis s.s. specimens from 20 localities were used for mtDNA analysis, and 346 specimens comprising 341 An. sinensis s.s. from 22 localities and five Anopheles kleini Rueda from one locality were examined in the microsatellite study. Neighbor-joining analysis of pairwise FST and RST based on microsatellite results showed that the populations are divided into two groups, as did the mtDNA results. However, the Bayesian analysis and factorial correspondence analysis plots showed three distinct clusters. Among the mtDNA and microsatellite results, only microsatellites represented small but positive and significant isolation-by-distance patterns. Both molecular markers show the Taebaek and Sobaek Mountain ranges as barriers between the northern and southern parts of the ROK. The newly recognized third group suggests possible introgressive hybridization of An. sinensis s.s. with closely related species. The slightly different composition of populations in each group based on different markers is probably because of different population dynamics in each group. These results imply that there is restricted gene flow of epidemiologically important malaria-related genes between the northern and southern parts of the ROK.

Quantitative determination of enzalutamide, an anti-prostate cancer drug, in rat plasma using liquid chromatography-tandem mass spectrometry, and its application to a pharmacokinetic study.

This report details a method using liquid chromatography-tandem mass spectrometry (LC-MS/MS) that allows one to determine the concentration of an atypical anticancer drug, enzalutamide, in rat plasma. Specifically, this method involves the addition of an acetonitrile and bicalutamide (internal standard) solution to plasma samples. Following centrifugation of this mixture, an aliquot of the supernatant was directly injected into the LC-MS/MS system. Separation was achieved using a column packed with octadecylsilica (5 µm, 2.1 × 50 mm) with 10 mM ammonium acetate in acetonitrile as the mobile phase; detection was accomplished using MS/MS by multiple-reaction monitoring via an electrospray ionization source. This method demonstrated a linear standard curve (r = 0.997) over a concentration range of 0.001-1 µg/mL, as well as an intra- and inter-assay precision of 2.7 and 5.1%, respectively, and an accuracy range from 100.8 to 105.6%. The lower limit of quantification was 1.0 ng/mL in 50 µL of rat plasma sample. We also demonstrated that this analytical method could be successfully applied to the pharmacokinetic study of enzalutamide in rats.

Genetic Diversity of Dengue Vector Aedes albopictus Collected from South Korea, Japan, and Laos.

Aedes albopictus is native to Southeast Asia and has emerged as a major vector for vector-borne diseases that are spreading rapidly worldwide. Recent studies have shown that Ae. albopictus populations have different genetic groups dependent on their thermal adaptations; however, studies on Korean populations are limited. In this study, we analyzed the genetic diversity and structure of two mitochondrial genes (COI and ND5) and sixteen microsatellites in mosquitoes inhabiting Korea, Japan, and Laos. The results indicate that the Korean population has low genetic diversity, with an independent cluster distinct from the Laos population. Mixed clusters have also been observed in the Korean population. On the basis of these findings, two hypotheses are proposed. First, certain Korean populations are native. Second, some subpopulations that descended from the metapopulation (East Asian countries) were introduced to Japan before migrating to Korea. Furthermore, we previously demonstrated that Ae. albopictus appears to have been imported to Korea. In conclusion, the dengue-virus-carrying mosquitoes could migrate to Korea from Southeast Asian epidemic regions, where they can survive during the severe winter months. The key findings can be used to establish an integrated pest management strategy based on population genetics for the Korean Ae. albopictus population.

The polymorphism and the geographical distribution of the knockdown resistance (kdr) of Anopheles sinensis in the Republic of Korea.

BACKGROUND: In the Republic of Korea (ROK), six sibling species of the Anopheles sinensis complex are considered the vector species of malaria, but data on their susceptibilities to malaria and vector capacities have been controversial. The intensive use of insecticides has contributed to the rapid development and spread of insecticide resistance in the An. sinensis complex. Knockdown resistance (kdr) to pyrethroids and DDT in the An. sinensis complex is associated with a mutation in codon 1014 of the voltage-gated sodium channel (VGSC) gene. Because the degree of insecticide resistance varies among mosquito species and populations, the detection of kdr mutations among the six sibling species of the An. sinensis complex is a prerequisite for establishing effective long-term vector control strategies in the ROK METHODS: In order to investigate species-specific kdr mutations, An. sinensis complex specimens have been collected from 22 sites in the ROK. Because of the difficulties with species identifications that are based only on morphological characteristics, molecular identification methods have been conducted on every specimen. Part of the IIS6 domain of the VGSC was polymerase chain reaction-amplified and directly sequenced. RESULTS: The molecular analyses revealed that mutations existed at codon 1014 only in An. sinensis sensu stricto and no mutations were found in the other five Anopheles species. In An. sinensis s.s., one wild type (TTG L1014) and three mutant types (TTT L1014F, TTC L1014F, and TGT L1014C) of kdr alleles were detected. The TTC L1014F mutation was observed for the first time in this species. CONCLUSIONS: The fact that the highly polymorphic kdr gene is only observed in An. sinensis s.s., out of the six Anopheles species and their geographical distribution suggest the need for future studies of insecticide resistance monitoring and investigations of species-specific resistance mechanisms in order to build successful malaria vector control programmes in the ROK.

First record of the complete mitochondrial genome of Tubifex tubifex (Müller) 1774 (Annelida; Clitellata; Oligochaeta) and phylogenetic analysis.

The complete mitochondrial genome of Tubifex tubifex was analyzed using the MGISEQ-2000 platform. The size of the complete mitochondrial genome was 15,972 bp. Data pertaining to the genome, such as the presence of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a putative control region were submitted to NCBI (MW690579). A phylogenetic tree was constructed with the sequences of the 13 PCGs using the maximum-likelihood method. Despite only a few references available on the complete mitochondrial genome of other aquatic oligochaetes, our phylogenetic analysis revealed that the freshwater oligochaetes T. tubifex and Limnodrilus hoffmeisteri are in a cluster different from that of the earthworm group.

First record of the complete mitochondrial genome and phylogenetic analysis of Limnodrilus hoffmeisteri Claparède, 1862 (Annelida; Clitellata; Oligochaeta).

The complete mitochondrial genome of Limnodrilus hoffmeisteri was analyzed using the Illumina NovaSeq 6000 platform. The length of the complete mitochondrial genome was 15,972 bp. The sequencing data, comprising 13 protein coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a putative control region, were submitted to the National Center for Biotechnology Information (MW732144). A phylogenetic tree was constructed based on the sequences of 13 PCGs using the maximum likelihood method. To date, only a single study has been conducted on the complete mitochondrial genome of another aquatic oligochaete. This phylogenetic tree revealed that L. hoffmeisteri is clustered with Tubifex tubifex and forms a sister group to the earthworm group.

The complete mitochondrial genome of Nais communis Piguet, 1906 (Annelida; Clitellata; Naididae).

The complete mitochondrial genome of Nais communis was analyzed using the Illumina Hiseq 2000 platform. The length of the complete mitochondrial genome was 15,685 bp, and the data were submitted to NCBI (MW770354). The genome contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a putative control region. A phylogenetic tree was constructed based on the sequences of 13 PCGs identified by the maximum-likelihood method. Regardless of the lack of studies on the complete mitochondrial genome of other aquatic oligochaetes, the phylogenetic tree showed N. communis to cluster with Tubifex tubifex and Limnodrilus hoffmeisteri with high support value, and the freshwater oligochaete and earthworm groups to be sister groups.

Population genetic analysis reveals secondary contact between Eriocheir sinensis and E. japonica in South Korea.

BACKGROUND: The Chinese mitten crab (Eriocheir sinensis) and the Japanese mitten crab (E. japonica) of the family Varunidae, which are also critical fishery species in their native habitats, including China, Japan, and South Korea, exhibit a rare migration life history for the decapod life cycle. Eriocheir sinensis and E. japonica in South Korea may have originated from speciation or secondary contact in South Korea after speciation of these two species; however, the genetic relationship between these South Korean populations remains unclear, and need to be clarified. OBJECTIVE: This study examined the population genetic properties of E. sinensis and E. japonica in South Korea to reveal the origin of their co-existence. METHODS: Mitochondrial DNA cytochrome c oxidase I sequences of 120 E. sinensis and E. japonica from 6 sampling sites in South Korea were sequenced. Their genetic diversity and haplotype data were compared to previously reported data from the Chinese mainland, Taiwan, Japan, and Russia. RESULTS: The haplotype network, analysis of molecular variance, FST values, Mantel test, and Bayesian skyline plot results of South Korean E. sinensis and E. japonica demonstrated that E. sinensis and E. japonica were isolated from their central populations, Chinese and Japanese populations, by the distance due to the temperature, salinity, ocean current flow, or a geohistorical event. In addition, genetic analysis indicated that the South Korean populations of the two species were marginal populations, exhibiting low genetic diversity, significant negative neutrality values, and radial haplotype networks. The current results also suggest that the Geum River is an overlapping habitat for the natural populations of E. sinensis and E. japonica in South Korea. Further research is required to examine the geohistorical and evolutionary event between E. sinensis and E. japonica in South Korea. CONCLUSIONS: The co-existence of E. sinensis and E. japonica in South Korea may have originated from secondary contact after their speciation.

Cryptic diversity and population genetic structure of the mantis shrimp Oratosquilla oratoria in South Korea.

BACKGROUND: The Japanese mantis shrimp Oratosquilla oratoria has two genetic lineages in its Chinese and Japanese populations, which are considered cryptic species. However, the Korean O. oratoria populations have only been studied morphologically, and their genetic diversity pattern remains unknown. OBJECTIVE: To examine the genetic diversity of the Korean O. oratoria populations to explore its cryptic diversity and underlying processes. METHODS: We sequenced the mitochondrial cytochrome c oxidase I gene of 107 O. oratoria individuals from 8 sampling sites in South Korea. Their genetic diversity and haplotype data were compared to previously reported data from 16 Chinese and 6 Japanese populations. RESULTS: The haplotype network, analysis of molecular variance, FST values, and Bayesian skyline plot of the Korean O. oratoria populations confirmed that they were divided into two genetic lineages corresponding to the two previously identified cryptic species, which might be correlated to ocean currents and water temperature. In addition, the population genetic analysis indicated that both lineages had high genetic diversity. Although the Geoje region belongs to the southern group, it only contained lineage N, which could be related to the specific environmental characteristics of Geoje or the hybridization of the two lineages of O. oratoria. CONCLUSION: Korean O. oratoria populations have enough cryptic diversity to be described as cryptic species and are correlated with ocean currents and water temperatures. Lineage N dominance in Geoje might be related to environmental characteristics or hybridization.

Megadraconema cornutum, a new genus and species from Korea, with a discussion of its classification and relationships within the family Draconematidae (Nematoda, Desmodorida) based on morphological and molecular characters.

A new genus and species of Draconematidae Filipjev, 1918, Megadraconema cornutum gen. nov., sp. nov., inhabiting subtidal sediments in Jejudo, Korea is described. Megadraconema cornutum gen. nov., sp. nov. is mainly characterized by a long body (1630-2220 µm), presence of a transverse circle of well-developed papillae-like cuticular protrusions at the base of the lip region, a head capsule with reticular structure of subcuticle, an amphid with a pore-like opening, and an internal, bar-shaped fovea. The diagnosis of the family Draconematidae is emended and a key to genus is provided based on their major differential diagnostic characteristics, summarized in a table. Phylogenetic relationships of all the genera within the Draconematidae are discussed for the first time, based on molecular analyses and morphological features. The phylogenetic position of the new genus and relationships within the family Draconematidae based on analysis of molecular sequence data are examined. Analysis of 18S rRNA gene sequences does not support the currently accepted classification, and indicates paraphyly of the subfamily Draconematinae.

Complete mitochondrial genome of Aedes flavopictus (Yamada, 1921) (Diptera: Culicidae) collected in South Korea.

In this study, we determined for the first time the mitochondrial genome sequence of an Aedes flavopictus specimen collected in South Korea. Its mitochondrial genome was 16,060 bp in length, consisting of 13 protein-coding, 22 tRNA, and 2 rRNA genes and a non-coding A + T rich region. The overall base composition in the heavy strand was 39.7, 8.6, 12.7, and 39% of A, G, C, and T, respectively, and the G + C content was 21.2%. Phylogenetic analysis revealed that Aedes spp. formed a monophyletic clade.

Comparative population genetics of the invasive mosquito Aedes albopictus and the native mosquito Aedes flavopictus in the Korean peninsula.

BACKGROUND: Aedes mosquitoes are important invasive species contributing to the spread of chikungunya, dengue fever, yellow fever, zika virus, and other dangerous vector-borne diseases. Aedes albopictus is native to southeast Asia, with rapid expansion due to human activity, showing a wide distribution in the Korean peninsula. Aedes flavopictus is considered to be native to East Asia, with a broad distribution in the region, including the Korean peninsula. A better understanding of the genetic diversity of these species is critical for establishing strategies for disease prevention and vector control. METHODS: We obtained DNA from 148 specimens of Ae. albopictus and 166 specimens of Ae. flavopictus in Korea, and amplified two mitochondrial genes (COI and ND5) to compare the genetic diversity and structure of the two species. RESULTS: We obtained a 658-bp sequence of COI and a 423-bp sequence of ND5 from both mosquito species. We found low diversity and a nonsignificant population genetic structure in Ae. albopictus, and high diversity and a nonsignificant structure in Ae. flavopictus for these two mitochondrial genes. Aedes albopictus had fewer haplotypes with respect to the number of individuals, and a slight mismatch distribution was confirmed. By contrast, Ae. flavopictus had a large number of haplotypes compared with the number of individuals, and a large unimodal-type mismatch distribution was confirmed. Although the genetic structure of both species was nonsignificant, Ae. flavopictus exhibited higher genetic diversity than Ae. albopictus. CONCLUSIONS: Aedes albopictus appears to be an introduced species, whereas Ae. flavopictus is endemic to the Korean peninsula, and the difference in genetic diversity between the two species is related to their adaptability and introduction history. Further studies on the genetic structure and diversity of these mosquitos will provide useful data for vector control.

First record of the complete mitochondrial genome of the mantis shrimp, Gonodactylaceus randalli (Manning, 1978) (Stomatopoda: Gonodactylidae).

Biofouling has long been known as a major route for the invasion by non-indigenous species. The mantis shrimp, Gonodactylaceus randalli, is the first stomatopod species that has been identified in a biofouling community. In this study, we sequenced and analyzed the complete mitochondrial genome sequence of this species for the first time. Its mitochondrial genome is 15,907 bp in length and comprises 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding A + T-rich region. The overall base composition in the heavy strand is as follows: A: 37.3%, T: 31.3%, G: 11.9%, and C: 19.4%, with a G + C content of 31.3%. The phylogenetic analysis revealed that G. randalli belonged to the families Protosquillidae, Gonodactylidae, and Takuidae, in the same clade, within the superfamily Gonodactyloidea. This is the first record of the complete mitochondrial genome sequence of the genus Gonodactylaceus.

Complete mitochondrial genome of Cyclograpsus intermedius Ortmann, 1894 (Crustacea: Decapoda: Grapsoidea) specimen collected in South Korea.

In this study, the complete 16,184 bp mitochondrial genome of Cyclograpsus intermedius was determined from a specimen collected in South Korea. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and a non-coding A + T rich region. The base composition of the heavy strand in the mitochondrial genome was 34.7% A, 10.7% G, 18.7% C, and 35.9% T, resulting in a G + C content of 29.4%. A maximum-likelihood phylogenetic tree based on the 13 mitochondrial protein-coding genes showed that C. intermedius clustered together with the Varunidae. These molecular data will be useful for studying the evolutionary relationships among crab species.

Complete mitochondrial genome of the commensal scale worm, Arctonoe vittata (Grube, 1855) (Polychaeta: Polynoidae), collected from benthic habitat of the eastern coast of Korea.

The complete mitogenome sequence of the commensal polynoid scale worm Arctonoe vittata was determined for the first time in the present study. The total length of the newly sequenced mitogenome was 15,125 bp, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The phylogenetic position of A. vittata was examined by maximum likelihood analysis using concatenated 13 protein-coding genes with 18 selected polychaete species. Arctonoe vittata was nested within the suborder Aphroditiformia and closely related to Aphrodita australis among the selected species. The newly determined mitogenome sequence will be useful for further phylogenetic and evolutionary studies of this group.

Complete mitochondrial genome of the mantis shrimp Taku spinosocarinatus (Fukuda, 1909) (Stomatopoda: Gonodactyloidea: Takuidae) in South Korea.

The superfamily Gonodactyloidea is polyphyletic because of Hemisquillidae, but to date, mitochondrial genome of that family does not exist. As valuable data that can be compared in the future with that family within this superfamily, we report the first complete mitochondrial genome sequence of Taku spinosocarinatus of the family Takuidae. The mitochondrial genome is 15,960 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding A + T rich region. The overall base composition in the heavy strand was as follows: A: 34.2%, G: 13.4%, C: 19.8%, and T: 32.6%, with a G + C content of 33.2%. Phylogenetic analysis revealed that this species was most closely related to Gonodactylus chiragra of Gonodactylidae, registered with NCBI to date. The result of this study will enable additional comparisons between families in the future.

Complete mitochondrial genome of the mantis shrimp, Chorisquilla orientalis Hwang, Ahyong, & Kim, 2018 (Stomatopoda: Protosquillidae).

In this study, we determined the mitochondrial genome of a stomatopod, Chorisquilla orientalis, collected from Korean waters. The complete mitochondrial genome comprised 15,880 bp, encoding 13 proteins, 22 transfer RNAs, 2 ribosomal RNAs genes, and a non-coding A + T rich region. The overall base composition in the heavy strand was A: 35.5%, G: 12.4%, C: 18.3%, and T: 33.7%, with a G + C content of 30.8%. Phylogenetic analysis showed that C. orientalis belonged to the families Gonodactylidae and Takuidae in the same clade, and to the superfamily Gonodactyloidea within Stomatopoda. This is the first record of the complete mitochondrial genome sequence of the family Protosquillidae.

Phylogeographic studies on two shore crab species from East Asia: similar but different stories.

BACKGROUND: The genetic structure of marine organisms in the East Asian region has long been a subject of interest. Two grapsid crab species, Hemigrapsus penicillatus (De Haan, 1835) and Hemigrapsus sanguineus (De Haan, 1835), are commonly found in the rocky intertidal zones around this region. They are known to spread via larval migration, which makes them an appropriate model species for observing the genetic structure of East Asian intertidal invertebrate animals. OBJECTIVE: We investigated the genetic structure of the East Asian crabs H. penicillatus and H. sanguineus. METHODS: We collected specimens of H. penicillatus from seven locations (42 individuals) and of H. sanguineus from ten locations (58 individuals) in Korea, Japan, and Taiwan. We investigated and compared the genetic diversity and structure of populations of these species using mitochondrial cytochrome oxidase subunit I (COI) sequences. RESULTS: Our results show that both species are genetically structured between South Korea and Japan, and that the Taiwan population forms a cluster that is separate from those of the other countries. Populations of H. penicillatus contain less genetic diversity than those of H. sanguineus. CONCLUSION: These results suggest that there is a genetic structure between the two species at present in East Asia.