Characterization and phylogenetic analysis of the complete mitochondrial genome of the red alga, Gracilaria eucheumatoides Harvey 1860 (Gracilariales: Gracilariaceae) from Vietnam.

The marine red alga, Gracilaria eucheumatoides, is economically significant for its agar production and pharmacologically active compounds. This study reveals its complete mitochondrial genome (mitogenome), sequenced using Illumina's next-generation technology. The mitogenome is a 25,909 bp circular molecule with a G + C content of 27.21%, comprising 24 protein-coding genes, two ribosomal RNA genes, 24 transfer RNA genes, and one open reading frame (ORF) with an unidentified function. Both gene structure and composition are highly conserved within Gracilaria. The phylogenetic analyses fully support a close relationship of G. eucheumatoides with other Gracilaria species, as well as its sister relationship with G. urvillei. This mitogenome sequencing effort of G. eucheumatoides provides crucial data for future phylogenetic research on marine red algae.

The complete mitochondrial genome of the sand bubbler crab Scopimera longidactyla Shen 1932 (Decapoda: Dotillidae) and its phylogenetic analysis.

The sand bubbler crab, Scopimera longidactyla Shen, 1932 (Arthropoda: Malacostraca: Decapoda: Thoracotremata: Dotillidae), is commonly found along tropical and subtropical sandy shores of China, Korea, and Taiwan. Ecologically, it plays an important role in the productivity of sandy shores through their feeding and burrowing activities. In this study, the first complete mitochondrial genome (mitogenome) of S. longidactyla was analyzed using next-generation sequencer. Its mitogenome, circular in structure, spans 15,965 bp with a GC content of 29.97%, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one putative control region. Its mitogenome arrangement and composition are identical to its two congeners, S. globosa and S. intermedia. Phylogenetic analysis fully supports for the monophyly of the genus Scopimera and the sister relationship between S. longidactyla and S. globosa. The complete mitogenome of S. longidactyla and its phylogenetic implications will provide valuable insights for further studies in phylogenetic and evolutionary biology.

Genetic Structure and Diversity of Hatchery and Wild Populations of Yellow Catfish Tachysurus fulvidraco (Siluriformes: Bagridae) from Korea.

Yellow catfish Tachysurus fulvidraco is an important commercial fish species in South Korea. However, due to their current declines in its distribution area and population size, it is being released from hatchery populations into wild populations. Hatchery populations also produced from wild broodstocks are used for its captive breeding. We reported 15 new microsatellite DNA markers of T. fulvidraco to identify the genetic diversity and structure of its hatchery and wild populations, providing baseline data for useful resource development strategies. The observed heterozygosity of the hatchery populations ranged from 0.816 to 0.873, and that of the wild populations ranged from 0.771 to 0.840. Their inbreeding coefficient ranged from -0.078 to 0.024. All populations experienced a bottleneck (p < 0.05), with effective population sizes ranging from 21 to infinity. Their gene structure was divided into two groups with STRUCTURE results of K = 2. It was confirmed that each hatchery population originated from a different wild population. This study provides genetic information necessary for the future development and conservation of fishery resources for T. fulvidraco.

Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids.

Background: As hybridization can reduce biodiversity or cause extinction, it is important to identify both purebred parental species and their hybrids prior to conserving them. The Suwon tree frog, Dryophytes suweonensis, is an endangered wildlife species in Korea that shares its habitat and often hybridizes with the Japanese tree frog, D. japonicus. In particular, D. suweonensis, D. japonicus, and their hybrids often have abnormal ovaries and gonads, which are known causes that could threaten their existence. Methods: We collected 57 individuals from six localities where D. suweonensis is known to be present. High-resolution melting curve (HRM) analysis of the mitochondrial 12S ribosomal RNA gene was performed to determine the maternal species. Thereafter, the DNA sequences of five nuclear genes (SIAH, TYR, POMC, RAG1, and C-MYC) were analyzed to determine their parental species and hybrid status. Results: The HRM analysis showed that the melting temperature of D. suweonensis was in the range of 79.0-79.3 °C, and that of D. japonicus was 77.7-78.0 °C, which clearly distinguished the two tree frog species. DNA sequencing of the five nuclear genes revealed 37 single-nucleotide polymorphism (SNP) sites, and STRUCTURE analysis showed a two-group structure as the most likely grouping solution. No heterozygous position in the purebred parental sequences with Q values ≥ 0.995 were found, which clearly distinguished the two treefrog species from their hybrids; 11 individuals were found to be D. suweonensis, eight were found to be D. japonicus, and the remaining 38 individuals were found to be hybrids. Conclusion: Thus, it was possible to unambiguously identify the parental species and their hybrids using HRM analysis and DNA sequencing methods. This study provided fundamental information for D. suweonensis conservation and restoration research.

The complete mitochondrial genome of the bait worm, Marphysa victori (Annelida; Polychaeta; Eunicida; Eunicidae).

The complete mitochondrial genome of Marphysa victori Lavesque, Daffe, Bonifácio & Hutchings, 2017, was 15,891 bp in length with a GC content of 41%, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The maximum-likelihood tree showed the closest relationship between M. victori and M. sanguinea.

The complete mitochondrial genome of soft coral, Eleutherobia rubra (Brundin, 1896) (Cnidaria; Anthozoa; Malacalcyonacea; Alcyoniidae).

The mitogenome of a soft coral, Eleutherobia rubra (Brundin, 1896), was completely sequenced for the first time. The total mitogenome length of E. rubra is 18,724 bp with 14 protein-coding genes, two ribosomal RNA genes, one transfer RNA gene (tRNA-Met), and one non-coding region (NCR). The gene order is also consistent with other Alcyoniidae species. The base composition is 30.1% A, 16.7% C, 19.5% G, and 33.7% T, with a G-C content of 36.2%. This is the first record of the complete mitogenome sequence of the genus Eleutherobia.

Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe.

BACKGROUND: The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced. OBJECTIVE: To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea. METHODS: The mitogenome was characterized using the primer walking method with phylogenetic relationships. RESULTS: The complete mitogenome of G. naktongensis Geum River was 16,607 bp, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA (tRNA) genes. Seventeen substitutions were found by comparing the tRNA regions between G. naktongensis Geum and Nakdong Rivers and G. pappenheimi; most were specific to G. naktongensis Nakdong River, with changes in their secondary structures. The comparison between G. naktongensis Geum River and G. pappenheimi revealed differences in the lengths of the D-loop and two tRNAs (tRNAArg and tRNATrp) and the secondary structures in the TΨC-arm of tRNAHis. In the phylogenetic tree, G. naktongensis Geum River did not cluster with its conspecific specimen from the Nakdong River in South Korea, but showed the closest relationship to G. pappenheimi in mainland China. CONCLUSIONS: Our results support the existence of the Paleo-Huanghe River connecting the Korean peninsula and mainland China, suggesting that G. naktongensis in the Geum River should be treated as a different evolutionarily significant unit separated from that in the Nakdong River. The complete mitogenome of G. naktongensis Geum River provides essential baseline data to establish strategies for its conservation and restoration.

The complete mitochondrial genome of Tachysurus nitidus (Siluriformes: Bagridae) from the Geum river in Korea.

The complete mitochondrial genome of a bagrid catfish, Tachysurus nitidus was completely analyzed by the primer walking method. It was composed of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region with a total length of 16,537 bp. In the phylogenetic tree, using mitochondrial genome of 13 related sequences revealed that T. nitidus (MW451217) of Korea is clustered with T. nitidus (KC822643) of China. This complete mitochondrial genome provides an important resource for reviewing the phylogenetic relationships and taxonomic status of the bagrid species.

Occurrence and Molecular Identification of Microcotyle sebastis Isolated from Fish Farms of the Korean Rockfish, Sebastes schlegelii.

Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.

The complete mitochondrial genome of Montipora efflorescens (Scleractinia: Acroporidae).

The complete mitogenome of the Sclreractinia, Montipora efflorescens Bernard, 1897 was sequenced for the first time. It had 17,887 bp, with 13 protein-coding genes, and two rRNA and two tRNA genes. Composition of M. efflorescens mitogenome was identical to that of typical Scleractinians. In conclusion, the complete mitogenome may provide detailed information on coral phylogeny.

The full-length mitochondrial genome of Tachysurus fulvidraco (Siluriformes: Bagridae) from Geum river in Korea.

The full-length mitochondrial genome of the yellow catfish, Tachysurus fulvidraco was analyzed by the primer walking method. Its assembled mitochondrial genome was found to be 16,527 bp, consisting of 37 genes (13 protein-coding genes, 22 tRNA gens, and 2 rRNA gens). The gene content and order of T. fulvidraco were congruent with those of typical vertebrate fishes. In the phylogenetic tree, it showed the closet relationship to the another conspecific specimen from China and Pseudobagrus koreanus and well separated from the other species in the family Bagridae.

The complete mitochondrial genome of blue-lined octopus Hapalochlaena fasciata (Hoyle, 1886) (Octopodiformes; Octopoda; Octopodidae).

The complete mitochondrial genome of the highly venomous blue-lined octopus, Hapalochlaena fasciata (Hoyle, 1886), was analyzed by the primer walking method. Its mitogenome was 15,479 bp in total length, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 23 transfer RNA genes. In the phylogenetic tree, the gene content and order were congruent with those of typical octopodiform species. The mitogenomic sequence presented could be very useful as the first record of the complete mitogenome for the genus Hapalochlaena.

The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae).

The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae) was analyzed by the primer walking method. The mitogenome was 17,451 bp in total length, comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was congruent with those of the other crocodile icefish but different with those of typical vertebrates. In the phylogenetic tree, C. dewitti showed the closest relationship to Chaenocephalus aceratus in the same family.

The full-length mitochondrial genome of the Fernholm's hagfish, Myxine fernholmi (Myxini; Myxiniformes; Myxinidae).

The full-length mitochondrial genome of the Fernholm's hagfish, Myxine fernholmi (Myxini; Myxiniformes; Myxinidae) was analyzed by the primer walking method. Its mitogenome was 18,862 bp in total length and was composed of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The gene content and order were congruent with those of typical vertebrates. In the phylogenetic tree, M. fernholmi showed the closest relationship to M. glutinosa in the same genus and subfamily and well separated from the other hagfish in the subfamily Eptatretinae.

The full-length mitochondrial genome of Cobitis nalbanti (Teleostei: Cypriniformes: Cobitidae).

The entire mitochondrial genome of Cobitis nalbanti (Teleostei: Cypriniformes: Cobitidae) was analyzed using the primer walking method. The mitogenome was 16,631 bp in length, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was congruent with those of typical vertebrates. In the phylogenetic tree, C. nalbanti was clearly separated from C. lutheri, which supported the recent taxonomic revision.

The complete mitochondrial genome of Alveopora japonica (Scleractinia: Acroporidae).

Here, for the first time, we sequenced the complete mitogenome of Alveopora japonica Eguchi, 1968 (Scleractinia: Acroporidae). Genome size was 17,886 bp with 13 protein-coding, two rRNA, and two tRNA genes. This gene composition was identical to the typical scleractinian pattern. Our results strongly support the recent transfer of this coral species to the family Acroporidae.

Full-length mitochondrial genome of the triton trumpet Charonia lampas (Littorinimorpha: Ranellidae).

The full-length mitochondrial genome of the triton trumpet Charonia lampas (Linnaeus, 1758) was analyzed by the primer walking method. Its mitogenome is 15,382 bp in length, comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order of C. lampas is congruent with those previously reported for the infraorder Littorinimorpha. This is the first full-length mitogenome sequence for the genus Charonia. In the phylogenetic tree, C. lampas formed a monophyletic group with the other species of the superfamily Tonnoidea, but did not show the closest phylogenetic relationship to a species from the same family, Ranellidae.

Complete sequence analysis of the mitochondrial genome of Auriculastra duplicata (Mollusca, Gastropoda, Ellobiidae).

The mitochondrial genome of the gastropod Auriculastra duplicata was completely sequenced. It was 13,920 bp in length and comprised 37 genes; two rrn genes and 22 trn genes. Phylogenetic analyses based on the concatenated protein-coding genes depicted the polyphyly of all species belonging to the family Ellobiidae; however, monophyly was observed among all species belonging to the subfamily Ellobiinae, in which A. duplicata clustered consistently with Auriculinella bidentata.

Phylogenetic relationships of Pseudorasbora, Pseudopungtungia, and Pungtungia (Teleostei; Cypriniformes; Gobioninae) inferred from multiple nuclear gene sequences.

Gobionine species belonging to the genera Pseudorasbora, Pseudopungtungia, and Pungtungia (Teleostei; Cypriniformes; Cyprinidae) have been heavily studied because of problems on taxonomy, threats of extinction, invasion, and human health. Nucleotide sequences of three nuclear genes, that is, recombination activating protein gene 1 (rag1), recombination activating gene 2 (rag2), and early growth response 1 gene (egr1), from Pseudorasbora, Pseudopungtungia, and Pungtungia species residing in China, Japan, and Korea, were analyzed to elucidate their intergeneric and interspecific phylogenetic relationships. In the phylogenetic tree inferred from their multiple gene sequences, Pseudorasbora, Pseudopungtungia and Pungtungia species ramified into three phylogenetically distinct clades; the "tenuicorpa" clade composed of Pseudopungtungia tenuicorpa, the "parva" clade composed of all Pseudorasbora species/subspecies, and the "herzi" clade composed of Pseudopungtungia nigra, and Pungtungia herzi. The genus Pseudorasbora was recovered as monophyletic, while the genus Pseudopungtungia was recovered as polyphyletic. Our phylogenetic result implies the unstable taxonomic status of the genus Pseudopungtungia.

Phylogenetic relationships among three new Hemibarbus mitogenome sequences belonging to the subfamily Gobioninae (Teleostei, Cypriniformes, and Cyprinidae).

BACKGROUND AND AIMS: Here, we present the full-length mitogenome sequences of Hemibarbus labeo, Hemibarbus longirostris, and Hemibarbus mylodon - three fish species belonging to the subfamily Gobioninae (Teleostei, Cypriniformes, and Cyprinidae). H. mylodon is endemic to the Korean Peninsula and a critically endangered freshwater species because of various anthropogenic activities around its natural habitat. RESULTS: Overall characteristics of mitogenomes of the three Hemibarbus species were identical to previously known typical vertebrate mitogenomes. Bayesian inference of phylogeny recovered the monophyly of the subfamily Gobioninae with high posterior probability support, with the three Hemibarbus species forming a strongly supported monophyletic group. H. mylodon was placed at the basal position, and H. longirostris was separated from two monophyletic H. labeo types. CONCLUSION: Our findings are congruent with the previous taxonomic appraisal based on morphological analysis.