Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of the freshwater fish Traccatichthys pulcher (Cypriniformes: Nemacheilidae) from China.

ABSTRACT: This study aimed to sequence and annotate the complete mitochondrial DNA genome sequence of Traccatichthys pulcher. The mitochondrial genome comprised 16,583 bp, harboring 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The whole genome contained T (25.8%), C (26.9%), A (31.4%), and G (15.9%), showing an obvious AT bias (57.2%). Based on the concatenated protein sequences of 13 PCGs, a phylogenetic tree was reconstructed by the maximum likelihood method, and the topology revealed the monophyly of Traccatichthys, and the gathering of T. pulcher and M. pulcher. The mitochondrial DNA of T. pulcher (MZ853162.1) and M. pulcher (NC_031581.1) were aligned by the BLAST 2 sequences tool, which showed 97% similarity.

SUBMITTER: Chen XJ

PROVIDER: S-EPMC9341357 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of the freshwater fish Traccatichthys pulcher (Cypriniformes: Nemacheilidae) from China.

Chen Xiao Jiang XJ Song Lin L Liu Wen Zhao WZ

Mitochondrial DNA. Part B, Resources 20220729 7

This study aimed to sequence and annotate the complete mitochondrial DNA genome sequence of Traccatichthys pulcher. The mitochondrial genome comprised 16,583 bp, harboring 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The whole genome contained T (25.8%), C (26.9%), A (31.4%), and G (15.9%), showing an obvious AT bias (57.2%). Based on the concatenated protein sequences of 13 PCGs, a phylogenetic tree was reconstructed by the maximum likelihood metho ...[more]

PMID: 35923638

Similar Datasets

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

The complete mitochondrial genome of Triplophysa nanpanjiangensis Zhu and Cao 1988 (Cypriniformes: Nemacheilidae).

Project description:The genus Triplophysa is an ideal taxon for understanding geological evolution. In this study, for the first time, we report the complete mitochondrial genome of T. nanpanjiangensis Zhu and Cao 1988 using the Nanopore sequencing. It is a circular genome with a length of 16558 bp, comprising 22 tRNAs, 13 protein-coding genes (PCGs), two rRNAs, and one non-coding control region. The phylogenetic tree demonstrates that T. nanpanjiangensis is sister to Triplophysa zhenfengensis and placed within the genus Triplophysa. Our mitogenomic studies provide a new pathway for understanding the molecular phylogeny of the genus Triplophysa.

| S-EPMC10776044 | biostudies-literature

Characterization of complete mitochondrial genome of Oreonectes furcocaudalis (Cypriniformes, Balitoridae, Nemacheilidae).

Project description:Oreonectes furcocaudalis is a rare cave-dwelling loach that lives in the karst cave of Rongshui and Rong'an county, Southwestern China. In this study, the complete mitochondrial genome of O. furcocaudalis is sequenced using the Illumina Hiseq4000 platform with de novo strategy, with a circular molecule of 16,569 bp in size (GenBank accession number KX778472). It contains 13 protein-coding, 2 ribosomal RNA, 22 transfer RNA genes, and a 917 bp control region. Phylogenetic tree based on the complete mitogenome show that Oreonectes as a clade is close to the genus Lefua and Homatula.

| S-EPMC7800486 | 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

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

Project description: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%.

| S-EPMC7748834 | biostudies-literature

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

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 Triplophysa grahami Regan 1906 (Cypriniformes: Nemacheilidae) and phylogenetic analysis.

Project description:Triplophysa grahami Regan 1906 is a member of the family Nemacheilidae, Cypriniformes, and native loach in Yunnan. In this study, the complete mitochondrial genome (mitogenome) of T. grahami Regan 1906 was firstly reported and analyzed. The mitogenome of T. grahami Regan 1906 is 16,566 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (D-loop). The arrangement and orientation of protein coding genes and RNAs in T. grahami Regan 1906 are identical to other species of Nemacheilidae. The base composition of T. grahami Regan 1906 mitogenome was 29.25% A, 28.55% T, 25.03% C, and 17.17% G. The phylogenetic analysis based on the mitogenome showed that T. grahami Regan 1906 belongs to the clade of genus Triplophysa and the monophyly of Triplophysa is identified. This study contributed valuable genetic data for T. grahami Regan 1906 and explored the phylogenetic relationships in Nemacheilidae.

| S-EPMC11378653 | biostudies-literature

Using Species Groups to Approach the Large and Taxonomically Unresolved Freshwater Fish Family Nemacheilidae (Teleostei: Cypriniformes).

Project description:Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families.

| S-EPMC8869502 | biostudies-literature

The complete mitochondrial genome of Paranemachilus genilepis (Zhu 1983) (Cypriniformes: Nemacheilidae) and its phylogenetic status.

Project description:Paranemachilus genilepis (Zhu 1983) is a small and benthic loach species that mainly distributes in the Guangxi Province, China. To date, little was known about the genetic information of this species as no molecular sequence has been published. In this study, the complete mitochondrial genome of P. genilepis was reported using the Illumina MiSeq platform. The genome was 16,563 base pairs (bp) in length and its structure was identical to most genomes of bony fishes. Phylogenetic analyses supported two clades (I and II) among Nemacheilidae species and P. genilepis was sister to Oreonectes furcocaudalis.

| S-EPMC7655035 | biostudies-literature