Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The second complete mitogenome of Scolopsis ciliata (Perciformes, Nemipteridae) to analyze control region structure and intraspecific variation.

ABSTRACT: In this study, we reported the complete mitogenome of Scolopsis ciliata sampled from the Beibu Gulf, South China Sea. It was 16,734 bp in length and contained 37 canonical mitochondrial genes and 2 non-coding regions. Fifty-one single nucleotide polymorphisms and five insertion and deletions were detected between two S. ciliata mitogenomes, suggesting a high level of intraspecific genetic variation in the species. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), and conserved sequence block domain (CSB-1, CSB-2, and CSB-3). The phylogenetic analysis of 21 complete mitogenome sequences well supports the phylogenetic position of S. ciliata and reveals the phylogenetic relationship of the genus Scolopsis.

SUBMITTER: Wu RX

PROVIDER: S-EPMC7707376 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The second complete mitogenome of Scolopsis ciliata (Perciformes, Nemipteridae) to analyze control region structure and intraspecific variation.

Wu Ren-Xie RX Miao Ben-Ben BB Niu Su-Fang SF Zhai Yun Y Zhang Hao-Ran HR Liu Fang F Ou Chun-Xiao CX

Mitochondrial DNA. Part B, Resources 20191011 2

In this study, we reported the complete mitogenome of Scolopsis ciliata sampled from the Beibu Gulf, South China Sea. It was 16,734 bp in length and contained 37 canonical mitochondrial genes and 2 non-coding regions. Fifty-one single nucleotide polymorphisms and five insertion and deletions were detected between two S. ciliata mitogenomes, suggesting a high level of intraspecific genetic variation in the species. The control region contained termination associated sequence domain ...[more]

PMID: 33366067

Similar Datasets

The second complete mitogenome of Nemipterus virgatus to dissect control region structure and phylogenetic problem of the superfamily Sparoidea (Teleostei, Perciformes).

Project description:In this study, we determined the complete mitogenome of Nemipterus virgatus of which the length was 17,073 bp, including 37 canonical mitochondrial genes and 2 non-coding regions. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), conserved sequence block domain (CSB-1, CSB-2, and CSB-3), and tandem repeat sequence domain (TTD). Nine single nucleotide polymorphisms and three insertion of tandem repeat sequence (each length in 28 bp) were detected between two N. virgatus mitogenomes. The phylogenetic analysis showed that the families Nemipteridae, Sparidae, Centracanthidae, and Lethrinidae did not gather into a monophyly of superfamily Sparoidea in the neighbor-joining tree.

| S-EPMC7707243 | biostudies-literature

Complete mitogenome of Gobiopterus lacustris (Perciformes: Gobiidae).

Project description:In this study, combining the gonad transcripts of the both sexes by RNA-Seq with the DNA sequences by conventional PCRs, we have determined the complete mitogenome of Gobiopterus lacustris collected from the mangrove waters of the Leizhou Peninsula in tropical South China. This mitochondrial genome is 16593 bp in length and consists of 37 genes in the typical vertebrate mitochondrial gene arrangement. This study will contribute on the phylogenetics of genus Gobiopterus and the other genera of Gobiidae.

| S-EPMC7510680 | biostudies-literature

Complete mitochondrial genome and phylogenetic relationship of ornate threadfin bream, Nemipterus hexodon (Perciformes, Nemipteridae).

Project description:The complete mitochondrial genome of the ornate threadfin bream, Nemipterus hexodon, was first determined by the pairs-walking sequencing in this study. The circular mtDNA molecule was 17,115 bp in size and the overall nucleotide composition of H-stand was A (29.55%), T (27.36%), G (16.08%), and C (27.01%), with a slight bias towards A + T. The complete mitogenome encoded 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (an origin of L-strand replication and a control region). The Bayesian tree supported the phylogenetic position of N. hexodon, which provided useful information for phylogenetic relationship in genus Nemipterus.

| S-EPMC7687645 | biostudies-literature

The complete mitogenome of Paralonchurus dumerilii (Perciformes: Sciaenidae).

Project description:We herein describe the complete mitochondrial genome of Paralonchurus dumerilii (Sciaenidae) and infer its phylogenetic position within the family. The genome is 16,498 bp long and featured by 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and a control region (D-loop). Our phylogenetic analysis suggests a basal position of P. dumerilii as the sister group of the other species of Sciaenidae analyzed.

| S-EPMC9186350 | biostudies-literature

The complete mitogenome of the Lepturacanthus savala (Perciformes: Trichiuridae) from the Yellow Sea.

Project description:Lepturacanthus savala is a commercially important marine fish belonging to the family Trichiuridae, with a wide distribution in the Indian-Western Pacific coastal waters. In this study, the complete mitochondrial genome of L. savala has been determined by primer walking methods. The mitogenome is 17,146 bp in length containing 13 protein-coding genes, 2 ribosomal RNA genes, 21 transfer RNA genes, a control region, and an origin of light-chain replication region. The base composition is 28.9% for A, 29.0% for C, 15.7% for G, and 26.4% for T. The maximum-likelihood tree based on whole mitogenome showed that it is the closest related species of Trichiurus.

| S-EPMC7782197 | biostudies-literature

Complete mitochondrial genome of Parupeneus barberinus (Perciformes, Mullidae): mitogenome characterization and phylogenetic analysis.

Project description:Parupeneus barberinus is a tropical/subtropical reef-dwelling marine fish belonging to the family Mullidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of P. barberinus. The complete mitochondrial genome is 16,560 bp long and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 18 species showed that P. barberinus is clustered with P. multifasciatus and P. chrysopleuron and rooted with other Mullidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.

| S-EPMC7800887 | biostudies-literature

Scolopsislacrima, a new species of monocle bream (Teleostei, Perciformes, Nemipteridae) from New Caledonia.

Project description:The new monocle bream Scolopsislacrima sp. nov. is described from a single specimen (213.6 mm standard length) collected from Grande-Terre Island, New Caledonia. The new species closely resembles S.meridiana, both species having the upper part of the pectoral-fin base with reddish blotch when fresh, two bands across the top of the snout, a dorsal scaled area on the head reaching anteriorly to between the anterior margin of the eye and anterior nostril, a similar number of lateral-line scales, and absence of a small antrorse spine below the eye. However, S.lacrima sp. nov. is distinguished from S.meridiana by having diagonal lines on the body absent (vs. 18-20 diagonal lines in the latter), a dark longitudinal band below the lateral line (vs. longitudinal lines absent), the caudal fin central area not patterned (vs. with several dark horizontal lines), a narrower body and shallower caudal peduncle.

| S-EPMC6629716 | biostudies-literature

The complete mitogenome of the Greytail angelfish Chaetodontoplus poliourus and its phylogenetic relationships (Perciformes: Pomacanthidae).

Project description:The mitogenome of the Greytail angelfish Chaetodontoplus poliourus (Pomacanthidae) was decoded using next-generation sequencing techniques. The de novo assembled mitogenome consists of 16,961 bp, including 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. The gene arrangement is identical to the other available Pomacanthidae mitogenomes submitted to NCBI. The overall base composition of the C. poliourus mitogenome was estimated to be 28.0% A, 30.9% C, 15.8% G and 25.3% T. The phylogenetic analysis of the C. poliourus mitogenome suggests a closer genetic relationship with Vermiculated angelfish Chaetodontoplus mesoleucus as expected from their similar color patterns. The overall pairwise identity except D-loop is 93.7% for these two sister species. The decoding of the C. poliourus mitogenome has enriched gene database for further evolutionary studies and conservation assessments of this uncommon and newly described marine angelfish.

| S-EPMC8567932 | biostudies-literature

Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Parrotfishes (Perciformes: Scaridae).

Project description:In order to investigate the molecular evolution of mitogenomes among the family Scaridae, the complete mitogenome sequences of twelve parrotfish species were determined and compared with those of seven other parrotfish species. The comparative analysis revealed that the general features and organization of the mitogenome were similar among the 19 parrotfish species. The base composition was similar among the parrotfishes, with the exception of the genus Calotomus, which exhibited an unusual negative AT skew in the whole mitogenome. The PCGs showed similar codon usage, and all of them underwent a strong purifying selection. The gene rearrangement typical of the parrotfishes was detected, with the tRNAMet inserted between the tRNAIle and tRNAGln, and the tRNAGln was followed by a putative tRNAMet pseudogene. The parrotfish mitogenomes displayed conserved gene overlaps and secondary structure in most tRNA genes, while the non-coding intergenic spacers varied among species. Phylogenetic analysis based on the thirteen PCGs and two rRNAs strongly supported the hypothesis that the parrotfishes could be subdivided into two clades with distinct ecological adaptations. The early divergence of the sea grass and coral reef clades occurred in the late Oligocene, probably related to the expansion of sea grass habitat. Later diversification within the coral reef clade could be dated back to the Miocene, likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work provided fundamental molecular data that will be useful for species identification, conservation, and further studies on the evolution of parrotfishes.

| S-EPMC10044791 | biostudies-literature

Mitogenome Announcement Characterization of the complete mitochondrial genome of golden tank goby, Glossogobius aureus (Perciformes: Gobiidae).

Project description:We applied next-generation sequencing (NGS) method to construct the complete mitochondrial genome of Glossogobius aureus. The obtained mitogenome of G. aureus (16,590 bp) exhibited a typical structure harboring 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control regions (D-loop). Most of mitochondrial genes are encoded on the heavy (H) strand, except for eight tRNAs and ND6. Unusual start codons were identified in COX1 (GTG) and ATP6 (TTG). Six genes (ND2, COX2, COX3, ND3, ND4, and CytB) were terminated by an incomplete stop codon (TA-/T-). A phylogenetic study showed that Glossogobius formed a clade distinct from other species in the subfamily Gobiinae. G. aureus was most closely related to G. giuris with 87.04% sequence identity among the four species in the genus Glossogobius.

| S-EPMC7759244 | biostudies-literature