Characterization of the complete chloroplast genome of Scrophularia cephalantha endemic to Korea.

Scrophularia species are highly valued and widely used traditional medicinal plants in East Asia. In this article, the complete chloroplast genome of Scrophularia cephalantha, a species endemic to South Korea, is reported for the first time. The genome is 153,016 bp long, and it is composed of a pair of 25,485 bp inverted repeats (IRs), separated by a large single copy (LSC) region of 84,124 bp, and a small single copy (SSC) region of 17,922 bp. There are 133 predicted genes in the genome, comprising 88 protein-coding genes, 37 tRNAs, and 8 rRNAs, with an overall GC content of 38%. Phylogenetic analysis based on the chloroplast genome data showed that S. cephalantha is a sister species to S. buergeriana and S. ningpoensis. The data provide useful molecular information for phylogenetic and evolutionary studies of the genus Scrophularia and its related species.

Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation.

The land snail Ellobium chinense (L. Pfeiffer, 1855) (Eupulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense. The results analyzed with COI and microsatellites revealed that E. chinense population exhibit metapopulation characteristics, retaining under the influence of the Kuroshio warm currents through expansion of the Late-Middle and Late Pleistocene. We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

Diversification and colonization processes in Gobioidei predicted based on mitochondrial 12S rRNA with focusing on Oxudercidae.

Gobioidei is one of the largest vertebrate taxa with over 2000 species observed around the globe. The largest group in Gobioidei is gobies that had been classified as one family, Gobiidae, based on morphological features. Molecular phylogenetic studies revealed that gobies consisted of two monophyletic families, Gobiidae and Oxudercidae, in which 19 lineages have been proposed, despite some claims arisen about the relationship among these lineages or species. We analyzed 58 Gobioidei species, including 45 East Asian oxudercids, based on 12S rRNA sequences to reconstruct the spatiotemporal diversification history of gobies. Our analysis yielded the results compatible with the previous reports in a large framework. The common ancestor of Gobiidae and Oxudercidae were estimated to appear at 38.66 Mya. Genus-level splits occurred in Gobiidae and Oxudercidae predominantly at Miocene and late Miocene to early Pleistocene, respectively. Gobies have likely originated in many parts of the northern and western Pacific Ocean, of which a large proportion of Oxudercidae have adapted to various environments in the North Pacific.

The complete mitochondrial genome of Plumarella spinosa (Octocorallia: Calcaxonia: Primnoidae) from South Korea.

Plumarella spinosa (Anthozoa: Octocorallia: Primnoidae) is an endangered marine soft coral species discovered on a 50-100 m deep reefs in South Korea. We analyzed the mitochondrial genome sequence of this species. The genome size was 19,037 bp in length consisting of 14 protein coding genes (PCGs), two rRNA genes and a tRNA gene. Our phylogenetic analysis for this species with 33 Octocorallia species reconstructed based on the nucleotide sequences of 14 PCGs showed that P. spinosa was placed as a sister to Narella hawainensis and Primnoidae formed a monophyletic group.

The complete mitochondrial genome of an Asian crested ibis Nipponia nippon (Pelecaniformes, Threskiornithidae) from South Korea.

The complete mitochondrial genome sequence from the Asian crested ibis, Nipponia nippon (Aves, Pelecaniformes, Threskiornithidae), was determined and characterized in detail. This mitochondrial genome is 16,813 bp long, and consists of 13 PCGs, 22 tRNAs, and 2 rRNAs. The nucleotide composition is slightly biased with A + T contents of 53.79% (A, T, C, and G was 30.37%, 23.42%, 31.99%, and 14.22%, respectively). 11 PCGs are initiated by ATN codons, except for cox1 and cox2 with GTG instead. The phylogenetic relationships based on the maximum-likelihood and Bayesian methods showed that the placement of N. nippon within the order Pelecaniformes, with forming the monoclade of the family Threskiornithidae.

Characterization of the complete mitochondrial genomes and phylogenetic analysis of the two Luciogobius species (Perciformes, Gobionellinae) from Korea.

The complete mitochondrial genomes of Luciogobius grandis and Luciogobius elongatus (Perciformes, Gobionellinae) living on rocky coasts in South Korea are reported here for the first time. The mitogenomes of L. grandis and L. elongatus have total lengths of 16,477 bp and 16,486 bp, respectively, and include 13 PCGs, small and large rRNAs, a control region, and 22 tRNAs. Most of the genes are encoded on the heavy strand except for nine genes. Compared with other Gobionellinae species, the PCGs of the two Luciogobius species have a conserved gene order. These data provide useful molecular information for phylogenetic studies concerning Luciogobius species and related species.

Complete mitochondrial genome of the Endangered species Ellobium chinense (Pulmonata, Ellobiidae) from Korea.

The complete mitochondrial genome of Ellobium chinense (Ellobioidea, Ellobiidae), an Endangered species in South Korea, is reported here for the first time. The mitogenome of E. chinense is 13,979 base pairs in total length and includes 13 PCGs, small and large rRNAs, and 21 tRNAs. Twelve genes are encoded on the light-strand and 24 genes on the heavy-strand. Compared to four other ellobiid species, the PCGs of E. chinense have a conserved gene order except for the positions of ND4L and ND4. These data provide useful molecular information for phylogenetic studies concerning ellobiids and related species.

DNA Barcoding of Metazoan Zooplankton Copepods from South Korea.

Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis-Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae-Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica-Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica-Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.

Sequence and organization of the complete mitogenome of a Siberian stone loach, Barbatula toni (Dybowsky, 1869) (Cypriniformes: Balitoridae).

In this study, we determined the complete mitogenome sequence of Siberian stone loach, Barbatula toni (Dybowsky, 1869). The total length of mitogenome is 16 623 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The genome organization and gene order were identical to that of the typical vertebrates. The control region harbors conserved sequence blocks (CSB-D, E, F, CSB-1, CBS-2 and CBS-3) and TA-nucleotide microsatellite repeats in its 3' end. The complete mitogenome may provide important molecular data for further phylogenetic analyses for higher taxa of teleost fishes, especially for the fishes in order Cypriniformes.

Complete mitochondrial genome of the mulberry white caterpillar Rondotia menciana (Lepidoptera: Bombycidae).

The mulberry white caterpillar, Rondotia menciana, belongs to the lepidopteran family Bombycidae, in which the domestic silkworm, Bombyx mori is included. In this study, we describe the complete mitochondrial genome of R. menciana in terms of general genomic features and characteristic features found in the A+T-rich region. The 15,364 bp long genome consisted of a typical set of genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes) and 1 major non-coding A+T-rich region, with the typical arrangement found in Lepidoptera. Twelve of the 13 PCGs started with typical ATN codons, except for the COI, which began with CGA and twelve of 13 PCGs had complete stop codons, except for the COII, which ended with a single T. The 360 bp long A+T-rich region harbored the conserved sequence blocks typically found in lepidopteran insects. Additionally, the A+T-rich region of R. menciana contained one tRNA(Met)-like structure, which had a proper anticodon and secondary structure.

Complete mitochondrial genome of the hydrothermal vent tubeworm, Ridgeia piscesae (Polychaeta, Siboglinidae).

The complete mitochondrial genome of Ridgeia piscesae (Polychaeta, Siboglinidae), one of the dominant taxa in deep-sea hydrothermal vents, is reported here for the first time. The R. piscesae mitogenome is 15,002 bp in total length and includes 13 protein-coding gene sequences, small and large rRNA sequences and 22 tRNA sequences. All genes are encoded on the heavy strand. The mitochondrial genomes of R. piscesae and other six polychaete species have a conserved gene order.

Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta (Perciformes, Odontobutidae).

The complete mitochondrial genome of Odontobutis interrupta (Perciformes, Odontobutidae), a species endemic to South Korea, is reported here for the first time. The O. interrupta mitogenome is 16 802 base pairs in total length and includes 13 PCGs, small and large rRNAs, a control region and 22 tRNAs. Nine genes are encoded on the light strand and 29 on the heavy strand. The O. interrupta mitochondrial genome has a conserved gene order compared to four other Odontobutis species and Micropercops swinhonis, a closely related species. The data will provide useful molecular information for phylogenetic studies concerning Odontobutidae and its related species.

Complete mitochondrial genome of Hymeniacidon sinapium (Demospongiae, Halichondriidae).

The complete mitochondrial genome of Hymeniacidon sinapium (Demospongiae, Halichondriidae) is reported here for the first time. The H. sinapium mitogenome is 23,435 base pairs in total length and includes 14 protein-coding gene sequences, small and large rRNA sequences, and 25 tRNA sequences. All genes are encoded on the heavy strand without overlapping genes.

Molecular and morphological data reveal hybrid origin of wild Prunus yedoensis (Rosaceae) from Jeju Island, Korea: implications for the origin of the flowering cherry.

PREMISE OF THE STUDY: The subgenus Cerasus of the genus Prunus includes several popular ornamental flowering cherries. Of the hundreds of cultivars, P. ×yedoensis ('Somei-yoshino') is the most popular and familiar cultivar in Korea and Japan and is considered to be of hybrid origin. However, the hybrid origin of P. ×yedoensis and its relationship to wild P. yedoensis, naturally occurring on Jeju Island, Korea, are highly controversial. METHODS: We extensively sampled wild P. yedoensis, cultivated P. ×yedoensis, and numerous individuals from other species belonging to subgenus Cerasus on Jeju Island. Samples from 71 accessions, representing 13 species and one cultivar (P. ×yedoensis), were sequenced for nrDNA ITS/ETS (952 characters) and seven noncoding cpDNA regions (5421 characters) and subjected to maximum parsimony and maximum likelihood analysis. Additive polymorphisms in the ITS/ETS regions were confirmed by cloning amplicons from representative species. KEY RESULTS: The nuclear (ITS/ETS and G3pdh) and cpDNA data, along with several morphological characteristics, provide the first convincing evidence for the hybrid origin of wild P. yedoensis. The maternal parent was determined to be P. spachiana f. ascendens, while the paternal parent was unresolved from the taxonomically complex P. serrulata/P. sargentii clade. The presence of two kinds of ribotypes was confirmed by cloning, and the possible origin of cultivated P. ×yedoensis from wild populations on Jeju Island was also suggested. CONCLUSIONS: Bidirectional and multiple hybridization events were responsible for the origin of wild P. yedoensis. Extensive gene flow was documented in this study, suggesting an important role of reticulate evolution in subgenus Cerasus.

DNA barcode reference data for the Korean herpetofauna and their applications.

Recently, amphibians and reptiles have drawn attention because of declines in species and populations caused mainly by habitat loss, overexploitation and climate change. This study constructed a DNA barcode database for the Korean herpetofauna, including all the recorded amphibians and 68% of the recorded reptiles, to provide a useful, standardized tool for species identification in monitoring and management. A total of 103 individuals from 18 amphibian and 17 reptile species were used to generate barcode sequences using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and to compare it with other suggested barcode loci. Comparing 16S rRNA, cytochrome b (Cytb) and COI for amphibians and 12S rRNA, Cytb and COI for reptiles, our results revealed that COI is better than the other markers in terms of a high level of sequence variation without length variation and moderate amplification success. Although the COI marker had no clear barcoding gap because of the high level of intraspecific variation, all of the analysed individuals from the same species clustered together in a neighbour-joining tree. High intraspecific variation suggests the possibility of cryptic species. Finally, using this database, confiscated snakes were identified as Elaphe schrenckii, designated as endangered in Korea and a food contaminant was identified as the lizard Takydromus amurensis.

Complete mitochondrial genome sequence of the Korean water deer Hydropotes inermis argyropus (Cervidae, Capreolinae).

The complete mitochondrial genome sequence of Hydropotes inermis argyropus consists of 13 protein-coding, 22 tRNA, and two rRNA genes, and 1 control region (CR). Three overlaps among the 13 protein-coding genes were found: ATP8/ATP6, ND4L/ND4, and ND5/ND6. The CR was located between the tRNA-Pro and tRNA-Phe genes and is 928 bp in length. The typical conserved domains, such as TAS and CSB, were identified in the CR.

Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus.

BACKGROUND: Microsatellites, a special class of repetitive DNA sequence, have become one of the most popular genetic markers for population/conservation genetic studies. However, its application to endangered species has been impeded by high development costs, a lack of available sequences, and technical difficulties. The water deer Hydropotes inermis is the sole existing endangered species of the subfamily Capreolinae. Although population genetics studies are urgently required for conservation management, no species-specific microsatellite marker has been reported. METHODS: We adopted next-generation sequencing (NGS) to elucidate the microsatellite markers of Korean water deer and overcome these impediments on marker developments. We performed genotyping to determine the efficiency of this method as applied to population genetics. RESULTS: We obtained 98 Mbp of nucleotide information from 260,467 sequence reads. A total of 20,101 di-/tri-nucleotide repeat motifs were identified; di-repeats were 5.9-fold more common than tri-repeats. [CA](n) and [AAC](n)/[AAT](n) repeats were the most frequent di- and tri-repeats, respectively. Of the 17,206 di-repeats, 12,471 microsatellite primer pairs were derived. PCR amplification of 400 primer pairs yielded 106 amplicons and 79 polymorphic markers from 20 individual Korean water deer. Polymorphic rates of the 79 new microsatellites varied from 2 to 11 alleles per locus (H(e): 0.050-0.880; H(o): 0.000-1.000), while those of known microsatellite markers transferred from cattle to Chinese water deer ranged from 4 to 6 alleles per locus (H(e): 0.279-0.714; H(o): 0.300-0.400). CONCLUSIONS: Polymorphic microsatellite markers from Korean water deer were successfully identified using NGS without any prior sequence information and deposited into the public database. Thus, the methods described herein represent a rapid and low-cost way to investigate the population genetics of endangered/non-model species.