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This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.

Abstract The black shinner Pseudopungtungia nigra Mori, 1935 is an endangered fish endemic to Korea. It lives in the narrow basin of the Geumgang River, Mangyeonggang River, and Ungcheoncheon Stream, which flow into the West Sea of Korea. One population of P. nigra in Ungcheoncheon Stream has been locally exterminated once; it is now inhabiting the upper reaches of the dam through a restoration program. Efforts to identify and understand the genetic structure of these populations are important for conservation planning. Here, we analyzed genetic diversity using 21 microsatellite markers for 9 populations. The mean number of alleles ranged from 4.4 to 8.1, mean allelic richness ranged from 4.6 to 7.8, mean observed heterozygosity ranged from 0.519 to 0.702, and mean expected heterozygosity ranged from 0.540 to 0.763. All groups had recent and historical bottlenecks (P

Liobagrus geumgangensis is a novel Korean fish species endemic to the Geumgang and Mangyeonggang River basins on the Korean Peninsula. During a survey of L. geumgangensis, the discovery of Liobagrus mediadiposalis as a potential threat prompted an investigation into L. geumgangensis genetic diversity and structure. Three populations of L. geumagangensis and one population of L. mediadiposalis were investigated using a 1024-bp sequence in the cytb region of mitochondrial DNA. The Mangyeonggang River of L. geumagangensis displayed the lowest haplotype diversity (Hd) within a range of 0.000–0.337, with one to two haplotypes (h). The Jecheon region of the Geumgang River for L. geumagangensis population had the highest nucleotide diversity (π) and was within the range of 0.00000–0.00066. The h of L. mediadiposalis population was 3, the range of Hd was 0.292, and π was 0.00231. Tajima’s D (D) and Fu’s Fs (F) were negative and non-significant in the LgGJ population. The genetic structure of L. geumgangensis had no shared haplotypes among the three populations. The discovery of L. mediadiposalis in the Geumgang River suggests the necessity of non-habitat conservation and population management of fish farms to conserve L. geumgangensis.

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.

Persicaria maackiana (Regel) Nakai ex T. Mori (1922), a species of the Polygonaceae family, is an annual plant widely distributed in Northeast Asia. We aimed to sequence the complete chloroplast genome of P. maackiana using Illumina HiSeq paired-end sequencing. The chloroplast genome was determined to be 160,635 bp. The complete chloroplast genome contained 129 genes, including 84 protein-coding genes, 37 tRNA, and eight rRNA genes. Phylogenetic analysis of the chloroplast genome sequences of 15 Polygonaceae plants revealed that P. maackiana was most closely related to P. perfoliata. Our findings might be useful for future phylogenetic studies of Polygonaceae.

The spotted sleeper, Odontobutis interrupta, is a fish species endemic to Korea and shows potential as an aquaculture species. Nevertheless, the population size of this species has declined significantly in recent years. To characterize the population structure and genetic diversity of O. interrupta in Korea, we analyzed four microsatellite loci in twelve populations from four major river systems. The provenance of the population was investigated to discern the origin of the translocated populations. The genetic diversity of the microsatellite ranged from 0.440 to 0.756, showing a high level of diversity similar to that of other freshwater fishes. However, mitochondrial DNA analysis exhibited low genetic diversity (Hd: 0.000–0.674, π: 0.00000–0.00159). The FST values of microsatellites and mitochondrial DNA ranged from 0.096 to 0.498 and −0.046 to 0.951, suggesting genetic admixture among populations. All populations exhibited an effective population size of O. interrupta.

The Korean endemic aucha perch, Coreoperca herzi, belongs to the family Centropomidae. Thus far, studies on C. herzi have focused on mitochondrial genomes, egg development, and early life history, while studies on their genetic diversity or genetic structure are lacking. We investigated these aspects in this study using mitochondrial DNA data. Haplotypes were divided into the Hangang River, Nakdonggang River, Geumgang River, and southwest region water system populations. A translocated population, the Yangyang Namdaechun Stream, was confirmed to have originated from the Hangang River water system population based on haplotype distribution and genetic structure results. The FST of the mitochondrial DNA indicated distinct genetic differentiation in the Hangang, Nakdonggang, Geumgang, and southwest regions. According to COI and analyses, the analysis of molecular variance revealed a higher variance in the four water system groups (98.41%) than in the southwest region water system versus the Hangang River water system (80.27%) groups. This study presents basic data for conservation by providing extensive information on the genetic diversity, genetic structure, and translocation population of C. herzi.

We present the first report of the complete mitochondrial genome of Opsariichthys uncirostris amurensis, which consists of 16,613 base pairs harboring 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome is A (27.15%), C (27.15%), T (26.77%), G (18.92%). The complete mitogenome of O. uncirostris amurensis, which was most closely related to O. bidens in the Bayesian inference tree, provides a better understanding of the phylogeny of the genus Opsariichthys.

This study is the first to report the complete 15,262 base pair mitochondrial genome of Buccinum bayani, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome is A (29.87%), T (39.11%), G (15.86%), and C (15.16%), with a high AT content of 68.98%. Phylogenetic analysis showed that B. bayani was most closely related to B. undatum. The mitogenome of B. bayani will provide helpful information to further our phylogenetic and evolutionary understanding of the family Buccininae.

In this study, the complete mitochondrial genome of Norwegian skates imported to Korea was sequenced with a circular molecule of 17,121 bp, which consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNA genes, and a control region (D-loop). And among these sequences, 193 bp sequence in the D-loop of the genus Raja suggested the possibility of being used as a genetic marker for classification of Raja and Dipturus species. The BI phylogenetic tree by using the nucleotide sequences of 13 PCGs from 15 available mitogenomes of family Rajidae confirmed also that Norwegian skates imported to Korea form a group with Raja brachyura species with high branch value, and that this was a species of Raja brachyura. As above, these results would be expected to provide for the further understanding on the phylogenetic relationship, taxonomic classification and phylogeography of the family Rajidae.

Kichulchoia brevifasciata is an endangered fish that is distributed across the Goheung Peninsula, South Korea. This is the first report of the complete mitochondrial genome of K. brevifasciata, which consists of 16,646 bp with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome is A (29.57%), T (28.08%), G (16.54%), and C (25.80%), with a high A + T content of 57.65%. Phylogenetic analysis showed that K. brevifasciata was most closely related to K. multifasciatas.

This study reports the complete mitochondrial genome of a Pungtungia herzi (♀) × Pseudopungtungia nigra (♂) hybrid. The P. herzi (♀) × P. nigra (♂) mitochondrial genome consists of 16,601 bp with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete mitochondrial genome is 29.99% A, 26.97% T, 17.11% G, and 25.92% C. In the phylogenetic tree, P. herzi (♀) × P. nigra (♂) is closer to P. herzi than to P. nigra. Obtaining the complete mitogenome of P. herzi (♀) × P. nigra (♂) will provide useful data regarding P. herzi and P. nigra conservation and evolution.

The complete mitogenome of Sardinella zunasi was determined by next-generation sequencing. The S. zunasi mitogenome was a circular 16,307 bp molecule that contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region (D-loop). The gene arrangement was consistent with other Sardinella mitogenomes. The phylogenetic relationships of 29 Clupeoidei species based on 13 protein-coding genes from the available mitogenomes were analyzed. Sardinella zunasi clustered with Sardinella among Clupeidae, suggesting a closer relationship with this genus. These results will be useful for understanding the phylogenetic relationships, taxonomic classification, and phylogeography of the genus Sardinella relative to other genera of Clupeoidei.

We report the first complete mitochondrial genome of Odontobutis obscurus, which consists of 17,038 bp harboring 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome is A (30.63%), C (28.72%), T (25.70%), G (14.95%). The complete mitogenome of Odontobutis obscurus, most closely related to congeners in the Bayesian inference and maximum likelihood tree, provides a better understanding of the phylogeny of the genus Odontobutis.

The complete mitochondrial genome of Chionoecetes japonicus was sequenced using a specimen collected offshore in the East Sea. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop), with a total length of 16,060 bp. The overall nucleotide composition was 34.91% A, 17.29% C, 10.93% G, and 36.87% T, with 71.78% A + T. In the phylogenetic tree was constructed using maximum-likelihood and Bayesian inference analyses, C. japonicus and C. japonicus pacificus formed a genetic clade that was sister to C. opilio.

This study is the first to research to report the complete 16,496 bp mitochondrial genome of Micropogonias furnieri, which consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome is 27.26% A, 25.65% T, 16.46% G, and 30.63% C, with a high A + T content of 52.91%. Phylogenetic analysis showed that M. furnieri was most closely related to Sciaenops ocellatus. In this study, the mitogenome of M. furnieri will provide useful information for phylogenetic and evolutionary understanding in the family Sciaenidae.

This study is the first to research report the complete 16,563 bp mitochondrial genome of Coreoleuciscus aeruginos, which consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (D-loop). The overall base composition of the complete genome is 31.0% A, 28.04% T, 16.27% G, and 24.69% C, with a high A + T content of 59.04%. According to our phylogenetic analysis, C. aeruginos is most closely related to Coreoleuciscus splendidus.

Halocynthia hilgendorfi ritteri is an ascidian distributed on the coast of Geoje Island in Korea and found on rocks. The mitochondrial genome of Halocynthia hilgendorfi ritteri consists of 15,181 bp with 13 protein-coding genes, 2 ribosomal RNAs, 23 transfer RNA genes. The overall base composition of the complete genome is 22.94% A, 43.32% T, 25.72% G, and 8.02% C, with a high A + T content of 66.26%.

Microphysogobio rapidus is an endangered freshwater fish from Korea with a limited distribution in the Nakdong River. Here, we determined the mitochondrial genome of M. rapidus, which consisted of 16,603 bp with 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome was 29.96% A, 26.06% T, 17.24% G, and 26.74% C, with high A + T content of 56.02%.

The complete mitochondrial genome of the hybrid grouper Hyporthodus septemfasciatus (♀)×Epinephelus moara (♂) was obtained by next-generation sequencing. The mitochondrial genome was 16,499 bp long, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region (D-loop). The overall base composition is 28.62% A, 28.27% C, 16.27% G, and 26.84% T with 55.46% A þ T. In the maximum-likelihood (ML) phylogenetic analysis, the hybrid grouper belonged to the same clade as H. septemfasciatus (maternal inheritance). [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the hybrid grouper Hyporthodus septemfasciatus (♀)×Epinephelus moara (♂) was obtained by next-generation sequencing. The mitochondrial genome was 16,499 bp long, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region (D-loop). The overall base composition is 28.62% A, 28.27% C, 16.27% G, and 26.84% T with 55.46% A + T. In the maximum-likelihood (ML) phylogenetic analysis, the hybrid grouper belonged to the same clade as H. septemfasciatus (maternal inheritance).