The complete mitochondrial genome of Kumgang fat minnow Rhynchocypris kumgangensis (Cypriniformes, Leuciscinae) in Korea

Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China

Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.

The complete mitochondrial genomes of the Leuciscus baicalensis and Rutilus rutilus: a detailed genomic comparison among closely related species of the Leuciscinae subfamily

Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

Identification of warm temperature acclimation-associated 65-kDa protein-2 in Kumgang fat minnow Rhynchocypris kumgangensis

Warm temperature acclimation-associated 65-kDa protein (Wap65) is known to respond to elevated water temperatures and the corresponding gene from several fish species has been cloned. Expression of Wap65 gene is induced by various physiological stresses, such as increase in water temperature, immune response and heavy metal exposure. Two isolated Wap65 genes, Wap65-1 and Wap65-2, display distinct tissue distribution and physiological functions despite high sequence homology. In a previous study, we identified the Wap65-1 gene (kmWap65-1) from Kumgang fat minnow, Rhynchocypris kumgangensis, a small freshwater fish endemic to Korea. The kmWap65-1 gene showed sequence homology with teleost Wap65-1 and mammalian hemopexin, and was highly expressed in response to increased water temperature and bacterial lipopolysaccharide (LPS) exposure. Here, we isolated kmWap65-2 from liver tissue of Kumgang fat minnow and compared the expression profiles of both kmWap65 genes following exposure to various physiological stresses, including thermal changes, bacterial challenge, and environmental toxins. Notably, while kmWap65-1 expression was significantly increased in response to high water temperature, LPS, cadmium, and iron, kmWap65-2 displayed no alterations in expression at high water temperature. However, kmWap65-2 expression was upregulated slightly in response to LPS and highly in presence of copper, bisphenol A, and estradiol. Based on the collective findings, we propose that kmWap65-1 and kmWap65-2 are multifunctional proteins with distinct functions that could serve as useful biomarkers for assessing physiological stress and associated responses in Kumgang fat minnow.

Identification of a warm-temperature acclimation-associated 65-kDa protein encoded by a temperature- and infection-responsive gene in the Kumgang fat minnow Rhynchocypris kumgangensis

Water temperature is one of the most important factors in fish physiology; thus, it is important to identify genes that respond to changes in water temperature. In this study, we identified a warm- temperature acclimation-associated 65-kDa protein (Wap65) in the Kumgang fat minnow Rhynchocypris kumgangensis, a small, cold-freshwater fish species endemic to Korea. Kumgang fat minnow Wap65-1 (kmWap65-1) was cloned using polymerase chain reaction (PCR)-based strategies, and was found to be highly homologous with teleost Wap65-1 and mammalian hemopexin, a heme-binding protein that transfers plasma heme into hepatocytes. kmWap65-1 mRNA was expressed mainly in the liver and its expression levels were significantly increased by both short- and long-term exposure to high temperature, which was evaluated by real-time quantitative PCR. Furthermore, the expression levels of kmWap65-1 were highly elevated by exposure to bacterial lipopolysaccharide. These results indicate that kmWap65-1 expression is associated with environmental stresses such as increases in water temperature and bacterial infection. J. Exp. Zool. 325A:65-74, 2016. © 2015 Wiley Periodicals, Inc.

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 sequence of a Korean Pungtungia herzi (Cypriniformes, Gobioninae)

The mtDNA sequence of Pungtungia herzi in Korea comprises 16,599 nt and contains 37 genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs). The content and the arrangement of the genome of the Korean specimen were identical to that previously reported for a Japanese specimen, with 98.3% genetic similarity between the two complete mitogenomes. The pairwise distances of three complete mitogenomes obtained among Pungtungia herzi and Pseudopongtungia nigra. Pungtungia herzi and Pseudopongtungia tenuicorpa, and Pungtungia nigra and Pseudopongtungia tenuicorpa were 9.26%, 12.88% and 12.75%, respectively.

Complete mitochondrial genome of the rare hypogean gobiid, Luciogobius pallidus, from Korea

The rare hypogean gobiid, Luciogobius pallidus, inhabits mainly in groundwater, spring, or upper rocky tidal regions in Korea and Japan. In this paper, the complete mitochondrial genome sequence of L. pallidus was firstly determined. The gene composition and order of L. pallidus were similar to most of the other fishes. The total length of the rare hypogean gobiid mitochondrial genome is 16,480 bp, including 13 protein-coding genes, 22 tRNA, 2 rRNA and 1 control region (CR). All genes were encoded on the heavy (H)-strand, with the exceptions of ND6 and eight tRNA genes, as found in other vertebrates. The CR (833 bp in length) is located between the tRNA-Pro and tRNA-Phe genes and contains three central conserved sequence blocks (CSB-D, CSB-E and CSB-F), three conserved sequence blocks (CSB-1, CBS-2 and CBS-3), and its 3' end embeds a poly-T-nucleotide sequence.