Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Three mitochondrial genomes of freshwater fishes in the genus Squalidus (Cypriniformes: Gobionidae).

ABSTRACT: Mitochondrial genomes of Squalidus mantschuricus, S. chankaensis, and S. longifilis have been determined using Sanger sequencing (GenBank Accession No. MT767745-MT767747). The three mitochondrial genomes consist of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region with the length of 16,605, 16,611, and 16,607 bp. Phylogenetic analysis of the three species showed that S. mantschuricus is nested within a fully supported terminal clade with S. argentatus, and S. chankaensis is a sister group of S. mantschuricus, S. argentatus, and S. wolterstorffi. Squalidus longifilis is positioned in a clade with S. multimaculatus and S. gracilis.

SUBMITTER: Chai J

PROVIDER: S-EPMC7703701 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Three complete mitochondrial genomes of freshwater fishes in the genus Abbottina (Cypriniformes: Gobionidae).

Project description:Abbottina binhi has been misidentified as Abbottina rivularis in China for a long time. In this study, we determined three mitochondrial genomes of A. rivularis and A. binhi such that these data should contribute to molecular identifications of the two species. The size of new mitochondrial genomes was 16,609 or 16,599 bp with A + T bias of 55.7-56.5% in the base compositions. Our reconstructed phylogeny showed that A. rivularis and A. binhi formed a sister taxon relationship, and they together were a monophyletic group.

| S-EPMC7687625 | biostudies-literature

Two complete mitochondrial genomes of Paraleucogobio fishes (Cypriniformes: Gobionidae).

Project description:Freshwater fishes in the genus Paraleucogobio include two species, Paraleucogobio notacanthus and Paraleucogobio strigatus. In this study, we determined complete mitochondrial genomes of P. notacanthus and P. strigatus to clarify their phylogenetic positions. The two mitochondrial genomes showed similar gene arrangements, codon use, gene overlaps or gene intervals with the length of 16,596?bp and 16,598?bp. Our phylogeny revealed that P. notacanthus and P. strigatus were nested within Gnathopogon fishes. The findings indicate that Paraleucogobio is a junior synonym of Gnathopogon.

| S-EPMC7687540 | biostudies-literature

Four complete mitochondrial genomes of Saurogobio fishes (Cypriniformes: Gobionidae).

Project description:In this study, we determined complete mitochondrial genomes of Saurogobio gracilicaudatus, S. xiangjiangensis, S. gymnocheilus, and S. lissilabris so that these data could contribute to reconstruct interspecific phylogenetic relationships within the genus Saurogobio. The four mitochondrial genomes showed A + T bias (55.2-57.0%) of base compositions with the length from 16,594 to 16,608 bp. Phylogenetic relationships among Saurogobio fishes and their close relatives showed that the genus Saurogobio was a monophyletic group and it could be divided into two major groups.

| S-EPMC7687549 | biostudies-literature

Complete mitochondrial genome of Belligobio pengxianensis (Cypriniformes: Gobionidae).

Project description:Belligobio pengxianensis is a small fish endemic to the upper Yangtze River of China. In this study, the complete mitochondrial genome of B. pengxianensis is determined for the first time, and it should become a reference sequence to aid in species identification, biodiversity monitoring and conservation. The mitogenome has overall length of 16,610 bp and AT content of 55.23%, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding control region. The results of phylogenetic analyses show that B. pengxianensis is nested within the genus Hemibarbus.

| S-EPMC10044147 | biostudies-literature

Complete mitochondrial genome of Ladislavia taczanowskii (Cypriniformes: Gobionidae).

Project description:Mitochondrial genomes of two individuals of Tachanovsky's gudgeon Ladislavia taczanowskii have been determined on the basis of Sanger dideoxy sequencing. The gene compositions of two genomes contain 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region with the same length 16,614 bp. The phylogenetic tree reveals that the monotypic genus Ladislavia is a sister group of the subfamily Gobioninae within the family Gobionidae.

| S-EPMC8330723 | biostudies-literature

Complete mitochondrial genome sequence of Squalidus chankanensis tsuchigae (Cypriniformes: Cyprinidae).

Project description:We determined the complete mitochondrial genome sequence of Squalidus chankanensis tsuchigae (Cypriniformes: Cyprinidae). It is 16,603 bp long, with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNA genes, and 1 control region, which is 927 bp long, located between tRNApro and tRNAphe. The overall base composition is as follows: 29.98% A, 16.86% G, 25.44% T, and 27.72% C, with a slight AT bias. These results provide necessary data for phylogenetic studies on Squalidus species.

| S-EPMC7748813 | biostudies-literature

Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China.

Project description:The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.

| S-EPMC9318155 | biostudies-literature

Complete Mitochondrial Genomes of Baikal Oilfishes (Perciformes: Cottoidei), Earth's Deepest-Swimming Freshwater Fishes.

Project description:Sculpins are predominantly benthic sit-and-wait predators that inhabit marine and freshwaters of the Northern Hemisphere. In striking contrast to riverine relatives, sculpins endemic to Lake Baikal have diversified in both form and function, with multiple taxa having adaptations for pelagic and bathyal niches within the world's deepest lake. Baikal Oilfishes (Comephorus spp.) represent a highly apomorphic taxon with unique skeletal morphology, soft anatomy, and reproductive ecology. Selection for novel behavior and life history may be evident in genes responsible for organismal energy balance, including those encoding subunits of the electron transport chain. Complete mitochondrial genomes were sequenced for the Big Baikal Oilfish (Comephorus baicalensis) and Little Baikal Oilfish (Comephorus dybowskii). Mitochondrial genomes encode genes essential for electron transport, and data provided here will complement ongoing investigations of genome-to-phenome maps for teleost respiration and metabolism. Phylogenetic analyses including oilfish mitogenomes and all publicly available cottoid representative sequences are largely concordant with previous studies.

| S-EPMC5938752 | biostudies-literature

Quaternary geomorphological and climatic changes associated with the diversification of Iberian freshwater fishes: The case of the genus Cobitis (Cypriniformes, Cobitidae).

Project description:We studied the population genetic structure of Cobitis vettonica, an endangered freshwater fish species endemic to the Iberian Peninsula, in order to propose a biogeographic model of the responses of species to the multiple changes that occurred in the Iberian hydrological system during the Quaternary period. We also deciphered the relationship of C. vettonica with its sister species C. paludica, particularly in sympatric areas, and provide genetic information for conservation purposes. To achieve this goal, we analyzed both mitochondrial and nuclear data (the cytochrome b and the nuclear recombination activating 1 genes) and a battery of single-nucleotide polymorphisms (SNPs) of 248 individuals of C. vettonica or C. paludica from 38 localities, including some sympatric ones, covering the entire distribution area of C. vettonica. We highlight the important role played by the hydrogeomorphological processes and climatic changes that occurred in the Iberian Peninsula during the Quaternary on both the population structure of C. vettonica and its relationship with its sister species C. paludica. Our results support the genetic introgression of populations at the eastern limit of the distribution of C. vettonica. Furthermore, we postulate genetic introgression in sympatric areas. Finally, we propose the establishment or expansion of four Operational Conservation Units (OCUs) for C. vettonica, and highlight the threat faced by its populations due to the low level of genetic diversity detected for some of its populations and genetic introgression with C. paludica, which could eventually displace C. vettonica, resulting in a loss of diversity in this species.

| S-EPMC8888266 | biostudies-literature

Year-round spawning of three tropical Cypriniformes fishes in Southeast Asia.

Project description:Present knowledge on spawning seasonality of freshwater fishes in tropical Asia and their relationship with environmental factors remains limited. Three Southeast Asian Cypriniformes fishes, Lobocheilos ovalis, Rasbora argyrotaenia and Tor Tambra, found in rainforest streams in Brunei Darussalam were studied on a monthly basis for a period of 2 years. To assess spawning characteristics, seasonality, gonadosomatic index and reproductive phases were examined from 621 L. ovalis, 507 R. argyrotaenia and 138 T. tambra. This study also examined environmental factors such as rainfall, air temperature, photoperiod and lunar illumination that may influence the timing of spawning of these species. We found that L. ovalis, R. argyrotaenia and T. tambra were reproductively active throughout the year but did not find that spawning in these species were associated with any of the investigated environmental factors. Our study showed that the non-seasonal reproductive ecology found in the tropical cypriniform species is distinctly different from that of temperate cypriniforms, which are known to follow spawning seasonality, suggesting an evolutionary adaptation to ensure their survival in an unstable environment. The reproductive strategy and ecological responses found in the tropical cypriniforms might be shifted in response to climate change scenarios in the future.

| S-EPMC10238536 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data