Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next generation sequencing yields the complete mitochondrial genome of the darkfin hind Cephalopholis urodeta (Serranidae) from the Mischief Reef, South China Sea.

ABSTRACT: The complete mitochondrial genome of the Cephalopholis urodeta (Serranidae: Epinephelinae) was sequenced by next-generation sequencing method on the basis of one female specimen collected from coral reef areas at the Mischief Reef, South China Sea. The mitogenome is 16,593 bp in length, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a D-loop region. The overall content of A + T is 55.66%, which is significantly higher than the C + G content (44.34%). Among four bases, C shows the lowest frequency (15.99%). Phylogenetic tree based on the 13 protein-coding genes was constructed for analyzing the position of C. urodeta. The results provide useful insights into further studies on population genetics and phylogenetics of groupers.

SUBMITTER: Liu N

PROVIDER: S-EPMC8797725 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Next generation sequencing yields the complete mitochondrial genome of the darkfin hind Cephalopholis urodeta (Serranidae) from the Mischief Reef, South China Sea.

Liu Ning N Sun Dianrong D Shan Binbin B Liu Yan Y Wang Liangming L Huang Yingbang Y Yang Changping C

Mitochondrial DNA. Part B, Resources 20220127 1

The complete mitochondrial genome of the Cephalopholis urodeta (Serranidae: Epinephelinae) was sequenced by next-generation sequencing method on the basis of one female specimen collected from coral reef areas at the Mischief Reef, South China Sea. The mitogenome is 16,593 bp in length, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a D-loop region. The overall content of A + T is 55.66%, which is significantly higher than the C + G content (44.34%). Among four bases ...[more]

PMID: 35097215

Similar Datasets

Next-generation sequencing yields the complete mitogenome of the Shaw's sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis curtus, which is 17,702 bp in size and includes 13 protein-coding (PCGs), two rRNA genes, 22 tRNA genes, and two control regions. PCGs, with 13 genes, are 11,261 bp in length. All PCGs use as the start codon ATN except ND1 (CTA) and COX1 (GTG); ATP8, ATP6, ND4L, ND5, and Cytb use the typical stop codon TAA; but COX2 and ND4 with a single T-. Phylogeny recon-structed using the Bayesian inference (BI) method with 13 PCGs indicates that H. curtus at the root of Laticaudinae.

| S-EPMC7707276 | biostudies-literature

Complete mitochondrial genome of darkfin hind Cephalopholis urodeta (Perciformes, Epinephelidae).

Project description:Darkfin hind, Cephalopholis urodeta, belongs to the subfamily Epinephelinae. It is one of the most important fish species in coral-reef ecosystem. In this study, the complete mitochondrial (mt) genome of C. urodeta has been determined. It was 16,592 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions. The mitogenome sequence of C. urodeta shared 94% and 92% similarity to that of C. sonnerati and C.sexmaculata, respectively. Phylogenetic tree was made based on the concatenated sequences of 12 protein-coding genes on mtH-strand. All the results provide insights into the evolution in the subfamily Epinephelinae.

| S-EPMC7799697 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of the blue-banded sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis cyanocinctus, which is 17,750 bp in size and includes 13 protein-coding (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 control regions. PCGs, with 13 genes, is 11,427 bp in length. All PCGs use ATN as the typical start codon except COX1 with GTG; the TAG was found as the stop codon in ND1 and ND2, the AGA was found as the stop codon in COI and ND6, the TAA was found as the stop codon in ATP8, ATP6, ND4L, ND5 and Cytb; while other 3 PCGs stop with a single T. Phylogeny reconstructed using the Bayesian inference (BI) method with 13 PCGs indicates the presence of H. cyanocinctus at the root of Laticaudinae.

| S-EPMC7687521 | biostudies-literature

Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae).

Project description:The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.

| S-EPMC10855530 | biostudies-literature

Characterization of the complete mitochondrial genome of Cephalopholis miniata (Perciformes, Serranidae) and its phylogenetic analysis.

Project description:Cephalopholis miniata belongs to the family Serranidae of Perciformes, which is one of the most important species in coral-reef ecosystem. In this study, its complete mitochondrial genome is presented. The assembled mitogenome is 16,585 bp and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12S and 16S), and an AT-rich region (also called control region, CR). The overall base composition is 29.2% A, 26.1% T, 16.2% G, and 28.5% C, with an A + T bias of 55.3%. Except ND6 and eight tRNAs, all other mitochondrial genes are encoded on the heavy strand. Phylogenetic analysis shows that all species of the genus Cephalopholis cluster into a clade, including the newly sequenced mitogenome of C. miniata.

| S-EPMC8204979 | biostudies-literature

Next-generation sequencing yields the complete chloroplast genome of Abies yuanbaoshanensis, an endangered species from South China.

Project description:Abies yuanbaoshanensis is critically endangered and restricted in the Yuanbao Mountain of China, with no more than 900 surviving individuals. Here, we reported the complete chloroplast (cp) genome of A. yuanbaoshanensis. The complete chloroplast genome is 121,795 bp in size. In total, 114 genes were identified, including 68 peptide-encoding genes, 35 tRNA genes, 4 rRNA genes, 6 open reading frames, and 1 pseudogene. Thirteen genes contain introns. In phylogenetic analysis, both the ML and BI analyses supported the monophyly of the genus Abies. Our study will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.

| S-EPMC8843196 | biostudies-literature

Next-generation sequencing yields the complete chloroplast genome of Abies kawakamii.

Project description:Abies kawakamii is endemic to the island of Taiwan and has been listed as a threatened species in the Red List. In present study, we reported the complete chloroplast genome of A. kawakamii. The chloroplast genome is 121,290 bp in size. It was composed of 114 genes and they were 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene. Loss of ndh genes was identified in the genome of A. kawakamii. Inverted repeat sequences include trnS-psaM-ycf12-trnG and trnG-ycf12-psaM-trnS were recognized in 52-kb inversion points. The phylogenetic analysis confirms that the Abies species are strongly supported as monophyletic. The complete plastome of A. kawakamii will provide potential genetic resources for further conservation and management strategies.

| S-EPMC7510649 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of stony coral (Favites abdita).

Project description:In this study, the complete mitogenome sequence of stony coral, Favites abdita (Scleractinia), has been decoded for the first time by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,825 bp, has unique 13 protein-coding genes (PCGs), 2 transfer RNAs and 3 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral phylogeny.

| S-EPMC7800620 | biostudies-literature

Next-generation sequencing yields the complete chloroplast genome of Pleione forrestii (Orchidaceae).

Project description:Pleione forrestii is an endangered terrestrial orchid with significant ornamental values. Here, we report the first complete chloroplast genome of P. forrestii. The circular genome was 158,759 bp in length and consisted of a pair of inverted repeats (IR 26,429 bp), which were separated by a large single-copy region (LSC 87,236 bp) and a small single copy-region (SSC 18,665 bp). It contained 135 genes (115 unique), including 87 protein-coding genes, 38 tRNAs, and 8 rRNAs. The maximum likelihood phylogenetic analysis indicated that P. forrestii was sister to P. bulbocodioides and P. formosana.

| S-EPMC7687623 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of wattled crane (Bugeranus carunculatus).

Project description:In this study, the complete mitogenome sequence of wattled crane (Bugeranus carunculatus) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,679 bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for wattled crane phylogeny.

| S-EPMC7799669 | biostudies-literature