Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the endangered freshwater fish Microphysogobio rapidus (Cypriniformes, Cyprinidae) from Korea.

ABSTRACT: 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%.

SUBMITTER: Kim KR

PROVIDER: S-EPMC7748834 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome of the endangered freshwater fish Microphysogobio rapidus (Cypriniformes, Cyprinidae) from Korea.

Kim Kang-Rae KR Bang In-Chul IC

Mitochondrial DNA. Part B, Resources 20200108 1

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%. ...[more]

PMID: 33366595

Similar Datasets

Complete mitochondrial genome of freshwater fish, Microphysogobio jeoni (Actinopterygii, Cypriniformes, Cyprinidae), from South Korea.

Project description:In this study, we determined the complete mitochondrial genome sequences of cyprinid freshwater fish, Microphysogobio jeoni, belonging to the subfamily Gobioninae in the order Cypriniformes. The complete mitogenome of M. jeoni was 16,602 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The gene order was identical with other Microphysogobio species. The overall nucleotide composition of M. jeoni was A + T: 56.1% and G + C: 43.9%, with slightly AT bias. In the phylogenetic tree, M. jeoni and other congeneric species clearly formed a monophyletic clade, and each species distinguished against each other well.

| S-EPMC7748646 | biostudies-literature

Complete mitochondrial genome of the freshwater fish, Carassioides acuminatus (Cypriniformes, cyprinidae).

Project description:In this study, the complete mitochondrial genome of Carassioides acuminatus was first sequenced and annotated. The entire mitogenome is 16,579bp in length, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region (D-loop). The overall nucleotide composition of the C. acuminatus mitochondrial genome shows an obvious anti-G bias. The accuracy of the fresh sequences was verified by phylogenetic analysis. The complete mitochondrial genome of C. acuminatus is useful to population genetics and molecular systematics.

| S-EPMC7800034 | biostudies-literature

Complete mitochondrial genome of golden variant of freshwater fish Labeo rajasthanicus (Cypriniformes: Cyprinidae): endemic to India.

Project description:The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.

| S-EPMC10776062 | biostudies-literature

The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis.

Project description:In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the O. ovale mitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception of tRNASer(AGY), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed that Onychostoma and Acrossocheilus were classified into three clades. There was a mosaic relationship between Onychostoma and Acrossocheilus. Moreover, the phylogenetic tree analysis showed that O. rarum was the closest species to O. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses of Onychostoma and Acrossocheilus.

| S-EPMC10298739 | biostudies-literature

The complete mitochondrial genome of the endangered freshwater fish Kichulchoia brevifasciata in Korea.

Project description: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.

| S-EPMC7971205 | biostudies-literature

The complete mitochondrial genome of the endangered freshwater fish Odontobutis obscurus from Korea.

Project description: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.

| S-EPMC8967202 | biostudies-literature

Complete mitochondrial genome of near threatened fish species Osteobrama belangeri (Cypriniformes: Cyprinidae).

Project description:The complete mitochondrial genome of Osteobrama belangeri was obtained, using Illumina high-throughput NextSeq 500 with 2 × 150 bp sequencing of mitochondrial DNA. The mitochondrial genome of O. belangeri was 16,602 bp in length (GenBank Accession No. KY887473), comprised of 13 protein coding genes, 22 tRNA genes, 2 rRNA genes and a control region, i.e. D-loop. In present mitogenome, 11 short sequence repeats were identified and validated in silico. The arrangement of genes was found identical to other Cypriniformes fish mitogenomes, available in NCBI database. Phylogenetic relationship established in the present study also supported that genus Osteobrama is member of subfamily Cyprininae (tribe: smiliogastrini) not Cultrinae, which provide useful insights into taxonomic status of the genus.

| S-EPMC7800496 | biostudies-literature

Sequence identification and phylogenetic analysis of the mitochondrial genome of Microphysogobio kiatingensis (Cypriniformes: Cyprinidae).

Project description:Microphysogobio kiatingensis is endemic freshwater fish of China and mainly distributed in the middle and upper reaches of the Yangtze River. The complete mitogenome of M. kiatingensis was first determined by using the next-generation sequencing in present study. The circular mitogenome followed the expected pattern for vertebrates, being 16,603 bp in length. It contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one displacement loop (D-loop) locus and an origin of replication on the light-strand (OL). Most of the genes are encoded on the heavy strand except ND6 and eight tRNA genes. The overall base composition was 30.78% A, 26.09% T, 26.59% C, 16.54% G, with 56.87% AT. Thirteen intergenic spacers and nine gene overlaps exist in the complete mitochondrial genome. Phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences with two different methods (maximum likelihood and neighbour-joining analysis) indicated that M. kiatingensis was grouped in one clade with the same genus. The complete mitogenome of M. kiatingensis can provide a useful data for the further research in Gobioninae. Meanwhile, it also provides help for biological genetics and classification of species.

| S-EPMC7800506 | biostudies-literature

Complete mitochondrial genome of Schizothorax davidi (Teleostei: Cypriniformes: Cyprinidae).

Project description:This study provides a mitochondrial complete genome of Schizothorax davidi. The complete genome is 16,576 bp in length with an A + T content of 54.9%, which contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogenetic analysis indicated that S. davidi is closely related to Schizothorax lissolabiatus. These results contribute to explore the adaptation strategy of S. davidi on the conditions of Qinghai-Tibet Plateau.

| S-EPMC7707262 | biostudies-literature

Complete mitochondrial genome of Schizothorax gongshanensis (Cypriniformes: Cyprinidae).

Project description:In this study, the complete mitochondrial DNA of Schizothorax gongshanensis was determined. The complete genome is 16,591 bp in length which contains 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes, an origin of light-strand replication (OL) and a control region (D-Loop). The complete mtDNA sequence of S. gongshanensis provides a useful genetic marker for the studies on molecular systematics, population genetics and stock assessment.

| S-EPMC7800125 | biostudies-literature