Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Sardinops sagax (Jenyns, 1842) (Clupeiformes: Clupeidae) and phylogenetic analyses of sardines.

ABSTRACT: Pacific sardine Sardinops sagax (Jenyns, 1842), a sardine species that widely distributes in Pacific, is an important commercial species in many areas. In this study, we characterized the complete mitochondrial genome of S. sagax using next generation sequencing technology. The complete mitogenome of S. sagax was 16,883 base pairs (bp) in length and comprised 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (rRNA), and one control region (D-loop). Phylogenetic analysis indicated that sardine species included three clades (I, II and III) and S. sagax clustered with Sardinops melanostictus.

SUBMITTER: Tang F

PROVIDER: S-EPMC7995841 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete mitochondrial genome of Chinese Konosirus punctatus (Clupeiformes, Clupeidae) and phylogenetic studies of Clupeiformes.

Project description:The Dotted Gizzard Shad (Konosirus punctatus) was one of the most important commercial fish species in China, Japan and Korea. In this study, the complete mitochondrial genome of K. punctatus was presented. The full length of the mitochondrial genome was 16,705 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, one non-coding control region (CR) and one origin of replication on the light-strand. The total nucleotide composition of mitochondrial DNA was 25.79%A, 25.09%T, 29.05%C, 20.08%G, and AT was 50.88%. The mitochondrial genome provides an important resource for solving taxonomic problems and studying molecular evolution.

| S-EPMC7782019 | biostudies-literature

The complete mitochondrial genome of Sardinella zunasi (Clupeiformes: Clupeidae).

Project description:The complete mitogenome of Sardinella zunasi was determined by next-generation sequencing. The S. zunasi mitogenome was a circular 16,307 bp molecule that contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region (D-loop). The gene arrangement was consistent with other Sardinella mitogenomes. The phylogenetic relationships of 29 Clupeoidei species based on 13 protein-coding genes from the available mitogenomes were analyzed. Sardinella zunasi clustered with Sardinella among Clupeidae, suggesting a closer relationship with this genus. These results will be useful for understanding the phylogenetic relationships, taxonomic classification, and phylogeography of the genus Sardinella relative to other genera of Clupeoidei.

| S-EPMC7995902 | biostudies-literature

The Complete Genome Sequences of 5 Species of Sardinella (Clupeidae, Clupeiformes).

Project description:We present the complete genome sequences of 5 species of Sardinella. Illumina sequencing was performed on genetic material from wild-caught specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.

| S-EPMC10766431 | biostudies-literature

Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae).

Project description:The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth's history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.

| S-EPMC8380030 | biostudies-literature

The complete mitochondrial genome of Thryssa hamiltonii and phylogenetic analysis of Engraulidae (Clupeiformes; Clupeoidei).

Project description:This study aimed to elucidate the complete mitochondrial genome (mitogenome) of Thryssa hamiltonii (Clupeiformes: Engraulidae). The circular mitogenome is 16,737-bp-long, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding control region as observed in other vertebrates. The overall base composition is as follows: A, 30.69%; T, 24.86%; C, 28.17%; G, 16.29%; a slight A?+?T bias of 55.55%. Phylogenetic analysis of 16 species in family Engraulidae revealed that T. hamiltonii clustered in subfamily Engraulinae and is closely related to Lycothrissa crocodilus. The present data will contribute to future phylogenetic studies on members of family Engraulidae and conservation strategies for T. hamiltonii.

| S-EPMC7801017 | biostudies-literature

The complete mitochondrial genome of Engraulis ringens (Engraulidae, Clupeiformes) and phylogenetic studies of Engraulidae.

Project description:In this study, the complete mitochondrial genome of Engraulis ringens has been determined. The whole sequence is 16,690 bp in length and included the typical structure of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (control region and L-strand replication origin). The overall base composition includes A 26.65%, T 26.09%, C 28.13%, G 19.13%, with a slightly A + T bias of 52.74%. Moreover, the 13 PCGs encode 3797 amino acids in total. The phylogenetic analysis of E. ringens in the Engraulidae family was constructed based on 12 PCGs encoded by the heavy strand, and the result showed that E. ringens is most closely related to Engraulis japonicus and Engraulis encrasicolus.

| S-EPMC7707291 | biostudies-literature

The complete mitochondrial genome of Sardinella lemuru (Clupeinae, Clupeidae, Clupeoidei) and phylogenetic studies of Clupeoidei.

Project description:The complete mitochondrial genome of Sardinella lemuru was sequenced using PCR amplification and primer walking sequence method. The complete mitochondrial genome of S. lemuru was 16,616 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The overall base composition was A 25.04%, C 29.36%, G 20.40%, T 25.20%. In this study, the gene arrangement was consistent with other Sardinella mitochondrial genomes. Additionally, the phylogenetic relationships of 23 Clupeoidei species based on the complete genome was analyzed, and the result showed that S. lemuru firstly clustered with other two Sardinella species, S. albella and S. maderensis. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Clupeoidei.

| S-EPMC7800547 | biostudies-literature

A new species of sardine, Sardinellapacifica from the Philippines (Teleostei, Clupeiformes, Clupeidae).

Project description:A new sardine, Sardinellapacifica sp. n., is described on the basis of 21 specimens collected from the Philippines. The new species closely resembles Sardinellafimbriata (Valenciennes, 1847), both species having lateral scales with centrally discontinuous striae, a dark spot on the dorsal-fin origin, more than 70 lower gill rakers on the first gill arch, the pelvic fin with eight rays, and 17 or 18 prepelvic and 12 or 13 postpelvic scutes. However, the new species is distinguished from the latter by lower counts of lateral scales, pseudobranchial filaments, and postpelvic scutes (38-41, 14-19 and 12-13, respectively vs. 44-46, 19-22 and 13-14), and a shorter lower jaw (10.4-11.6% of standard length vs. 11.1-12.2%). Sardinellapacifica sp. n. is known only from the Philippines, whereas S.fimbriata is restricted to the Indian Ocean, although previously considered to be an Indo-West Pacific species, distributed from India to the Philippines.

| S-EPMC6422981 | biostudies-literature

The next-generation sequencing reveals the complete mitochondrial genome of Alosa sapidissima (Perciformes: Clupeidae) with phylogenetic consideration.

Project description:The complete mitochondrial genome of the Alosa sapidissima is presented in this study. The mitochondrial genome is 16,741?bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition of Epinephelus awoara mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand in descending order is 28.79% of G, 28.39% of T, 24.94% of A, and 17.88% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The phylogenetic analysis by maximum-likelihood (ML) method showed that the A. sapidissima has the closer relationship to between the A. alosa and A. pseudoharengus in the phylogenetic relationship.

| S-EPMC7799985 | biostudies-literature

The complete mitochondrial genome of Thryssa kammalensis (Clupeiformes: Engraulidae).

Project description:In this study, the complete mitochondrial genome (mitogenome) sequence of Thryssa kammalensis has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16 968 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, two ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence (TAS) domain, the central conserved sequence block domains (CSB-F, CSB-E and CSB-D) and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3). There are eight copies of tandem repeats of 38 bp in the control region, which contain TAS.

| S-EPMC7800865 | 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