Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Wang P

PROVIDER: S-EPMC7801017 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Wang Pengfei P Zhao Chao C Fan Sigang S Yan LuLu L Qiu Lihua L

Mitochondrial DNA. Part B, Resources 20180427 2

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 ...[more]

PMID: 33490519

Similar Datasets

The complete mitochondrial genome of Thryssa hamiltonii (Engraulinae, Engranlidae, Clupeoidei) and phylogenetic studies of Clupeoidei.

Project description:The complete mitochondrial genome of Thryssa hamiltonii has been determined. The whole sequence was 16,894?bp in length and included 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region (D-loop). The overall base composition is A 30.77%, C 27.97%, G 16.25%, T 25.01%, with a slightly A?+?T bias of 55.78%. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Three tandem repeat sequences were observed in the control region. Phylogenetic tree was constructed based on 13 protein-coding genes sequences of 21 clupeoidei species, and the result showed that T. hamiltonii is most closely related to T. dussumieri. These mitogenome sequence data will be useful for population genetics and phylogenetic analysis of the Clupeoidei.

| S-EPMC7800704 | biostudies-literature

Complete mitochondrial genome sequence of Thryssa kammalensis (Clupeiformes, Engraulidae).

Project description:In this paper, the complete mitochondrial DNA (mtDNA) sequence of Thryssa kammalensis was determined. The mitochondrial genome is 16,884 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region as those found in other vertebrates, with the gene identical to that of typical vertebrates. The overall base composition of the heavy strand is 31.07% A, 24.82% T, 28.33% C, and 15.78% G, with an AT bias of 55.89%. Phylogeny of T. kammalensis suggested more close relationship with Lycothrissa crocodilus and Setipinna taty. The complete mitogenome of this species can provide a basic data for the studies on population history, molecular systematics, phylogeography, stock evaluation, and conservation genetics.

| S-EPMC7799547 | 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

The complete mitochondrial genome of Thryssa setirostris (Engraulinae, Engranlidae, Clupeoidei) and phylogenetic studies of Clupeoidei.

Project description:The complete mitochondrial genome of Thryssa setirostris has been determined. The whole sequence was 16,926?bp in length and included 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). The overall base composition is A 29.88%, C 29.23%, G 16.77%, T 24.02%, with a slightly A?+?T bias of 54%. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Phylogenetic tree was constructed based on 13 protein-coding genes sequences of 21 clupeoidei species, and the result showed that T. setirostris is most closely related to T. dussumieri. These mitogenome sequence data will be useful for population genetics and phylogenetic analysis of the Clupeoidei.

| S-EPMC7799913 | 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

Sequence and phylogenetic analysis of the mitochondrial genome for the Northern Anchovy, Engraulis mordax (Engraulidae: Clupeiformes).

Project description:The northern anchovy, Engraulis mordax, is a small planktivorous fish from the northeastern Pacific Ocean that is an important forage for fishes, birds, and marine mammals, and is also the target of a commercial fishery. Here, we assembled a complete 16,664 bp genome for the E. mordax mitochondrion, which encodes for 12S and 16S rRNAs, 22 tRNAs, 13 protein-coding genes, and a 1016 bp D-loop in the characteristic arrangement of Order Clupeiformes. Phylogenetic analysis confirmed the evolutionary relatedness of E. mordax to other fishes of Family Engraulidae within Order Clupeiformes, but also indicated non-monophyly for the herring family, Clupeidae.

| S-EPMC7510572 | biostudies-literature

Characterization of the complete mitochondrial genome sequence of Coilia brachygnathus (Clupeiformes, Engraulidae) from Huai River and its phylogenetic position.

Project description:The complete mitogenome sequence of Coilia brachygnathus (Kreyenberg & Pappenheim, 1908) from Wabu Lake in Huai River Basin was annotated and characterized in this study. This mitochondrial genome is a circular DNA molecule of 16.896 bp in size with 57.52% AT content, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich region (control region) as other bony fishes. There are a total of 10 overlap locations and 15 intergenic spacer regions throughout the mitogenome of C. brachygnathus. All PCGs employed a standard ATG as a start codon, except cytochrome c oxidase 1 (cox1) with GTG. In addition, TAA or TAG was identified as the typical stop codon. A phylogenetic tree reconstructed with the maximum likelihood method depicted a clone relationship with eight species of genus Coilia and our previous study based on the amino acid sequences of 13 mitochondrial PCGs. The complete mitochondrial genome is a valuable resource in classifying and conserving C. brachygnathus.

| S-EPMC9278443 | 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

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

Project description: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.

| S-EPMC7995841 | biostudies-literature