The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae)

Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

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.

The complete mitogenome of Paratanakia chii (Cypriniformes; Cyprinidae)

Paratanakia chii is a bitterling fish of the genus Paratanakia, subfamily Acheilognathinae and family Cyprinidae. The mitochondrial DNA sequence of P. chii is reported in this paper. The complete mitochondrial genome of P. chii is 16,575 bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 displacement loop (D-loop). The genome sequence is consistent with those of most other carp. The majority of PCGs have AT- (Met) start codons and TA- end codons. The A + T contents of the genome, PCGs, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) are 56.92%, 58.07%, 56.34%, and 54.21%, respectively. Phylogenetic analysis showed that P. chii is most closely related to Tanankia himantegus. These data will benefit relative ecological and phylogenetic studies.

Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

Rhodeuscyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R.cyanorostris. The mitogenome of R.cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R.cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R.cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeuscyanorostris exhibits the closest phylogenetic relationship with R.pseudosericeus, R.amarus, and R.sericeus. This study discloses the complete mitochondrial genome sequence of R.cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.

Mitogenomics of Central American weakly-electric fishes

Electric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. This group (ca. 200 species) has originated in South America, and six species colonized the Central American Isthmus. Here, we assembled the complete mitochondrial genomes (mitogenomes) for three Central American electric fishes (i.e. Sternopygus dariensis, Brachyhypopomus occidentalis, and Apteronotus rostratus), and, based on these data, explored their phylogenetic position among Gymnotiformes. The three mitogenomes show the same gene order, as reported for other fishes, with a size ranging from 16,631 to 17,093 bp. We uncovered a novel 60 bp intergenic spacer (IGS) located between the COII and tRNA^Lys genes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genus Apteronotus belongs to the early diverging lineage of the order. Finally, we found high sequence divergence (13%) between our B. occidentalis specimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome of B. occidentalis represents a different South American species. Indeed, phylogenetic analyses using Cytochrome b gene across the genus placed the previously reported individual within B. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.

Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes

Sinorhodeus microlepis (S. microlepis) is recently described as a new species and represents a new genus Sinorhodeu of the subfamily Acheilognathinae. In this study, we first sequenced the complete mitogenome of S. microlepis and compared with the other 29 bitterling mitogenomes. The S. microlepis mitogenome is 16,591 bp in length and contains 37 genes. Gene distribution pattern is identical among 30 bitterling mitogenomes. A significant linear correlation between A+T% and AT-skew were found among 29 bitterling mitogenomes, except S. microlepis shows unusual AT-skew with slightly negative in tRNAs and PCGs. Bitterling mitogenomes exhibit highly conserved usage bias of start codon, relative synonymous codons and amino acids, overlaps and non-coding intergenic spacers. Phylogenetic trees constructed by 13 PCGs strongly support the polyphyly of the genus Acheilognathus and the paraphyly of Rhodeus and Tanakia. Together with the unusual characters of S. microlepis mitogenomes and phylogenetic trees, S. microlepis should be a sister species to the genus Rhodeu that might diverge about 13.69 Ma (95% HPD: 12.96-14.48 Ma).

Phylogeography, Historical Demography, and Genetic Structure of the Rose Bitterling, Rhodeus ocellatus (Kner, 1866) (Cypriniformes: Acheilognathidae), in East Asia

Yao-Feng Tsao, Wen-Wen Lin, Chia-Hao Chang, Takayoshi Ueda, Nian-Hong Jang-Liaw, Ya-Hui Zhao, and Hsiao-Wei Kao (2016) Rose bitterling, Rhodeus ocellatus, is a small cyprinid fish distributed in East Asia. To infer its phylogeography and genetic structure, specimens from Taiwan, China, and Japan were collected, and complete mitochondrial cytochrome b (cyt b) DNA sequences were amplified and sequenced. Phylogenetic analyses identified seven mitochondrial lineages (A-G). Among them, three lineages (A, B, and C) distributed in mainland China. Lineages D, E, and F distributed in Japan, Korea, and Taiwan, respectively. Lineage G distributed in both China and Japan. The results of the Bayesian Binary MCMC analysis (BBM) suggested that the most recent common ancestor of R. ocellatus was from Lower Yangtze region. Divergence times among lineages inferred by molecular clock ranged from 7.55 to 1.44 million years ago. We propose that topography and climate changes by uplift of the Tibetan Plateau in the Late Miocene-Pliocene and the glacial-interglacial cycles in the Pleistocene might account for population expansion and genetic differentiation. Divergence times among lineages A, B, and C in Yangtze River basin ranged from 7.55 to 2.27 million years ago that might result from changes of flow directions of rivers from westward to eastward driven by the uplift of the Tibetan Plateau. The glacial-interglacial cycles in the Pleistocene might further cause population expansion to the northward of lineage G at about 0.19 million years ago. Lineage D in Japan was dispersed from the mainland China before the opening of the Sea of Japan, and lineage F in Taiwan was dispersed from the mainland China through the land bridge in the Pleistocene. Because of the genetic differentiation is statistically significant among populations, protection of genetic diversity and distinctness of R. ocellatus should be considered in the future conservation management.

Molecular and Functional Characterization of Thioredoxin 1 from Korean Rose Bitterling (Rhodeus uyekii)

Thioredoxin is a multifunctional antioxidant enzyme that belongs to the reductase family. In this study, we cloned and characterized thioredoxin 1 cDNA from the Korean rose bitterling Rhodeus uyekii (RuTrx). The full-length RuTrx cDNA consists of 674 bp with a 324 nt open reading frame (ORF) encoding a 107 aa protein. The deduced RuTrx amino acid sequence indicated a characteristic redox active site, ³¹WCGPC³⁵. Pairwise alignment revealed RuTrx amino acid identity (55.1%–83.2%) with orthologs from various species of mammalia, amphibia, fish and bird. Phylogenetic analysis was conducted to determine the evolutionary position of RuTrx. Expression analysis showed that RuTrx transcripts were present in all of the tissues examined, and was high in the hepatopancreas of R. uyekii. During early development, the expression of RuTrx transcripts was increased. Recombinant RuTrx protein (rRuTrx) was tested for its capacity to serve as an antioxidant enzyme using a metal-catalyzed oxidation (MCO) system. The ability of rRuTrx to protect against supercoiled DNA cleavage due to oxidative nicking increased in a dose-dependent manner. In Raw264.7 cells, Dihydroethidium (DHE) staining for ROS production indicated the antioxidant activity of rRuTrx. Together, these findings suggest that RuTrx may play a role in maintaining the redox state balance in Korean rose bitterling R. uyekii.

Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China

The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.

The complete mitochondrial genome of Cherskii's sculpin (Cottus czerskii) (Scorpaeniformes: Cottidae)

The complete mitogenome sequence of Cherskii's sculpin (Cottus czerskii) is determined using long PCR. The genome is 16,534 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The overall base composition of the heavy strand is A (26.4%), C (30.1%), T (26.1%) and G (17.5%). The control region is 857 bp in length and the A + T content of the region is 61.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Cherskii's sculpin. Mitochondrial genome analyses based on MP, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 21 Actinopterygii species. It appears that no less than two major phyletic lineages were present in Actinopterygii. The main clades within the Perciformes and Scorpaeniformes supported are: a clade including the Scombridae, Kyphosidae and Percichthyidae; a clade (Cottidae) with the Trichodontidae as the sister taxon to Pholidae, Anarhichadidae and Zoarcidae, which was supported by bootstrap values of 92%. The five Cottus species formed a paraphyletic group with the high bootstrap value (100%) in all examinations.

The complete mitochondrial genome of Amur bitterling (Rhodeus sericeus) from China

The complete mitogenome sequence of Amur bitterling (Rhodeus sericeus) was determined using long PCR. The genome was 16,581 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand was A (28.9%), C (27.2%), T (26.6%), and G (17.3%). The control region was 925 bp in length and the A + T content of the region was 63.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur bitterling. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity to the 13 Cyprinidae species. It appeared that no less than three major phyletic lineages were present in Cyprinidae. A clade (Rhodeus and Tanakia) with the R. lighti and R. Sinensis as the sister taxon to Acheilognathus was supported by bootstrap values of 100%. The close relationship of Amur bitterling to other Rhodeus species, especially R. pseudosericeus, is consistent with the results confirmed using morphology analysis.

Fish Myogenic Regulatory Protein LUC7L: Characterization and Expression Analysis in Korean Rose Bitterling (Rhodeus uyekii)

Serine-arginine-rich nuclear protein LUC7L plays an important role in the regulation of myogenesis in mice. In the present study, we isolated and characterized the Korean rose bitterling Rhodeus uyekii Luc7l cDNA, designated RuLuc7l. The RuLuc7l cDNA is 1,688 bp long and encodes a 364-amino-acid polypeptide containing serine/arginine-rich region at the C-terminus. The deduced RuLuc7l protein has high amino acid identity (71-97%) with those of other species including human. Phylogenetic analysis revealed that RuLUC7L clustered with fish LUC7L proteins. The expression of RuLuc7l mRNA was high in the brain, kidney, and stomach of Korean rose bitterling. Expression of the RuLuc7l mRNA was detected from 1 day post-fertilization (dpf) and moderately increased until 21 dpf during the early development. Further investigations are required to elucidate the functional role of RuLUC7L in myogenesis in R. uyekii.

Characterization, expression profile, and promoter analysis of the Rhodeus uyekii vitellogenin Ao1 gene

The fish Vitellogenin (Vg) gene has been applied as a biomarker for exposure to estrogenic compounds in the aquatic environment. In this study, we cloned and characterized Vg cDNA from the Korean rose bitterling Rhodeus uyekii (Ru-Vg). The Ru-Vg cDNA encodes a 1424-amino-acid polypeptide that belongs to the VgAo1 family and contains a putative signal peptide, lipovitellin I, phosvitin, and lipovitellin II, but does not contain the vWFD domain or the C-terminal peptide. The deduced Ru-Vg protein has high amino acid identity (73.97%–32.17%) with fish Vg proteins. Pairwise alignment and phylogenetic analysis revealed that Ru-Vg is most closely related to Acheilognathus yamatsutae Vg. Ru-Vg transcripts were detected using quantitative polymerase chain reaction in all tissues tested, with the highest level of expression observed in the ovary. Ru-Vg mRNA was upregulated in R. uyekii hepatopancreas cells in response to treatment with 17β-estradiol (E2) or 17α-ethinylestradiol (EE2). Luciferase reporter expression, driven by the 5'-regulatory region of the Ru-Vg gene spanning from −1020 bp to the start codon was induced by the estrogen receptor and was synergistically activated by treatment with E2 or EE2. These results suggest that R. uyekii and the Ru-Vg gene may be useful as biomarkers for exposure to E2 or EE2.

The complete mitochondrial genome of Tanakia limbata (Cypriniformes: Cyprinidae)

Bitterling Tanakia limbata is a temperate freshwater fish, distributes in fast-flowing creeks in central and southern Japan. In this study, the complete mitochondrial genome of T. limbata is sequenced to be 16,565 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of T. limbata in descending order is A 28.2%, C 27.5%, T 26.3%, and G 18.0%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of T. limbata and the elucidation of evolutionary mechanisms in Cyprinidae.

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 freshwater fish, Rhodeus suigensis (Cypriniformes, Cyprinidae)

The complete mitochondrial genome was sequenced from the cyprinid freshwater fish, Rhodeus suigensis. The genome sequence was 16,733 bp in size, and the gene order and contents were identical with the congeneric species R. uyekii. Of 13 protein-coding genes (PGCs), 3 genes (CO2, CO3 and Cytb) had an incomplete stop codon as shown in R. uyekii. Fot the base composition, R. suigensis showed anti-G bias (13.66% and 12.37%) on the second and third positions of the PCGs.

Complete mitochondrial genome of the Korean bitterling Acheilognathus koreensis (Cypriniformes; Cyprinidae)

The complete mitochondrial genome was sequenced from the Korean bitterling Acheilognathus koreensis. The genome sequence was 16,563 bp in size, and the gene order and contents were identical with the same genera Acheilognathus signifier and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), four genes (CO2, CO3, ND4, and Cytochrome b) had incomplete stop codons. The base composition of A. koreensis showed anti-G bias (13.69%) on the third position of PCGs.

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

The Kumgang fat minnow (Rhynchocypris kumgangensis) is an endemic and critically endangered freshwater species in the Korean peninsula. Its genome is 16604 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (CR). The gene order and composition of R. kumgangensis was similar to that of most other vertebrates. The base composition of the H-strand in descending order was A (27.75%), C (27.58%), T (26.31%), and G (18.36%), with an AT content of 54.06%. Three overlapping regions among the 13 protein-coding genes were found (i.e. ATP8/ATP6, ND4L/ND4, and ND5/ND6). The CR was located between the tRNA-Pro and tRNA-Phe genes and was determined to be 932 bp in length. Typical conserved domains, such as termination associated sequence and conserved sequence blocks, were identified in the CR.

Molecular characterization of a tandem-repeat galectin-9 (RuGlec9) from Korean rose bitterling (Rhodeus uyekii)

Galectin-9 is a b-galactoside-binding lectin that regulates many cellular functions, ranging from cell adhesion to pathogen recognition. We isolated and characterized the cDNA of tandem-repeat galectin-9 (RuGlec9) from the Korean rose bitterling (Rhodeus uyekii), an endemic Korean fish belonging to the Acheilognathinae subfamily of the Cyprinidae family. RuGlec9 cDNA is 1486 bp long and encodes a polypeptide of 323 amino acids containing two carbohydrate-recognition domains connected by a linker peptide. The deduced amino acid sequence of RuGlec9 shows 45-84% amino acid sequence identity to other galectin-9 sequences, including those from mammals and fish. RuGlec9 appeared in a large cluster with other galectin-9 sequences from fish and is more closely related to galectin-9 from Danio rerio than to those of other fish and mammals. RuGlec9 mRNA was expressed highly in the testis, spleen, intestine, stomach, and liver, and moderately in the brain, kidney, ovary, and gills of normal Korean rose bitterling. RuGlec9 mRNA expression in the spleen was increased by lipopolysaccharide. These results suggest that RuGlec9 plays a role in innate immunity in Korean rose bitterling.

Complete mitochondrial genomes of two cockroaches, Blattella germanica and Periplaneta americana, and the phylogenetic position of termites

The mitochondrial genomes are one of the most information-rich markers in phylogenetics. The relationships within superorder Dictyoptera have been debated in the literature. However, the closely related termites (Isoptera) are retained as unranked taxon within the order Blattaria (cockroaches). In this work, we sequenced the complete mitogenomes of two cockroaches, reconstructed the molecular phylogeny and attempted to infer the phylogenetic position of termites in Blattaria more reliably. The complete mtDNA nucleotide sequences of the peridomestic American cockroach (Periplaneta americana L.) and the domestic German cockroach (Blattella germanica L.) are 15,025 and 15,584 bp in size, respectively. The genome shares the gene order and orientation with previously known Blattaria mitogenomes. Most tRNAs could be folded into the typical cloverleaf secondary structure, but the tRNA-Ser (AGN) of P. americana appears to be missing the dihydrouridine arm. Using nucleotide and amino acid sequences as phylogenetic markers, we proposed that termites should be treated as a superfamily (Termitoidea) of cockroaches. We suggested that Polyphagoidea was the sister group of Termitoidea in Blattaria and supported that the suborder Caelifera is more closely related to the Phasmatodea than to the suborder Ensifera of Orthoptera.

The complete mitochondrial genome of rock carp Procypris rabaudi (Cypriniformes: Cyprinidae) and phylogenetic implications

Rock carp, Procypris rabaudi (Tchang), is an endemic fish species in China. We sequenced the complete mitochondrial genome of it by high-fidelity polymerase chain reaction with conserved primers and primer walking sequencing method. The complete mitochondrial genome of rock carp is 16595 bp in length and contains 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of most other vertebrates. The origin of L-strand replication (OL) in rock carp mitochondrion is located in a cluster of five tRNA genes (WANCY region) with 35 nucleotides in length. The control region is located between the tRNA-Pro and tRNA-Phe genes and is 943 bp in length. Three conserved sequence blocks (CSB), an extended termination associated sequence (ETAS), an AT-repeat microsatellite sequence and a putative promoter sequence for H-strand transcription (HSP) were identified within this region. The microsatellite sequence has a very low variation, with only one repeat alteration in 50 checked individuals (from 12 to 13 repeats). The phylogenetic analysis for rock carp was performed with Bayesian and Maximum likelihood (ML) methods based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result suggested that traditional taxonomic barbines possibly originated more early than cyprininaes; rock carp was placed at the position between barbines and cyprininaes, while has a closer relationship with cyprininaes than barbines.