Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome sequence of E. suratensis revealed by next generation sequencing.

ABSTRACT: The complete mitochondrial genome of Etroplus suratensis, the Green chromide cichlid, was determined for the first time through NGS method. The genome is 16,467?bp (Accession no. KU301747) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on plus strand was A: 28.3%, G: 15.2%, C: 30.9%, T: 25.6%, and the A?+?T content 53.9%. The control region contains a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cichlid fish of India.

SUBMITTER: Mohanta SK

PROVIDER: S-EPMC7800130 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome sequence of E. suratensis revealed by next generation sequencing.

Mohanta Sudip K SK Swain Subrat K SK Das Sofia P SP Bit Amrita A Das Gargee G Pradhan Sanghamitra S Sundaray Jitendra K JK Jayasankar P P Ninawe A S AS Das Paramananda P

Mitochondrial DNA. Part B, Resources 20161121 1

The complete mitochondrial genome of Etroplus suratensis, the Green chromide cichlid, was determined for the first time through NGS method. The genome is 16,467 bp (Accession no. KU301747) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on plus strand was A: 28.3%, G: 15.2%, C: 30.9%, T: 25.6%, and the A + T content 53.9%. The ...[more]

PMID: 33473612

Similar Datasets

The complete mitochondrial genome of the fine flounder Paralichthys adspersus revealed by next-generation sequencing.

Project description:The complete mitochondrial genome of the fine flounder Paralichthys adspersus, was determined for the first time through Next Generation Sequencing (NGS) approach. The mitogenome (GenBank accession no. MW288827) has 17,060 bp in length and consisted of the well-known 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and the control region. The overall nucleotide composition of the whole mitogenome was A: 27.5%, C: 29.5%, G: 17.1%, and T: 25.9%. Phylogenetic analyses based on 12 protein-coding genes clustered P. adspersus in the monophyletic Paralichthyidae clade, showing the closest phylogenetic relationship with its congeneric species P. olivaceus.

| S-EPMC8425720 | biostudies-literature

The complete mitochondrial genome of Xizicus (Haploxizicus) maculatus revealed by Next-Generation Sequencing and phylogenetic implication (Orthoptera, Meconematinae).

Project description:Xizicus Gorochov, 1993, the quiet-calling katydid, is a diverse genus with 68 species in world, which includes more than 45 species in China, has undergone numerous taxonomic revisions with contradicting conclusions. In this study the complete mitochondrial genome of Xizicus (Haploxizicus) maculatus collected from Hainan for the first time was sequenced using the Next-Generation Sequencing (NGS) technology. The length of whole mitogenome is 16,358 bp and contains the typical gene arrangement, base composition, and codon usage found in other related species. The overall base composition of the mitochondrial genome is 37.0 % A, 32.2 % T, 20.2 % C, and 10.6 % G. All 13 protein-coding genes (PCGs) began with typical ATN initiation codon. Nine of the 13 PCGs have a complete termination codon, but the remaining four genes (COI, COIII, ND5, and ND4) terminate with an incomplete T. Phylogenetic analyses are carried out based on the concatenated dataset of 13 PCGs and two rRNAs of Tettigoniidae species available in GenBank. Both Bayesian inference and Maximum Likelihood analyses recovered each subfamily as a monophyletic group. Regardless of the position of Lipotactinae, the relationships among the subfamilies of Tettigoniidae were as follows: ((((Tettigoniinae, Bradyporinae) Meconematinae) Conocephalinae) Hexacentrinae). The topological structure of the phylogeny trees showed that the Xizicus (Haploxizicus) maculatus is closer to Xizicus (Xizicus) fascipes than Xizicus (Eoxizicus) howardi.

| S-EPMC6048180 | biostudies-literature

The complete chloroplast genome sequence of Echinocodon Lobophyllus (Campanulaceae) revealed by next-generation sequencing and phylogenetic implication.

Project description:The complete chloroplast genome sequence of Echinocodon lobophyllus was determined by Illumina pair-end sequencing. The results showed that the complete plastid genome was 169,419?bp in length, containing a large single copy (LSC) of 85,599?bp and a small single copy (SSC) of 8054?bp, which were separated by a pair of 37,883?bp inverted repeats (IRs). A total of 109 unique genes were annotated, including 75 protein coding genes, 30 tRNA genes, and 4 rRNA genes. Among these genes, 16 genes contained one or two introns. The overall GC contents of the plastid genome were 38.4%. A maximum likelihood phylogenetic analysis showed that E. lobophyllus and Codonopsis minima formed one clade at the base of the phylogenetic tree of Campanulaceae with a high support value.

| S-EPMC7800722 | biostudies-literature

The complete chloroplast genome sequence of Cremastra appendiculata (Orchidaceae) revealed by next-generation sequencing and phylogenetic implication.

Project description:The complete chloroplast genome sequence of Cremastra appendiculata, a rare and endangered species of China, was determined by Illumina pair-end sequencing. The results showed that the complete plastid genome was 160,494 bp in length, containing a large single copy (LSC) of 88,249 bp and a small single copy (SSC) of 21,457 bp, which were separated by a pair of 25,394 bp inverted repeats (IRs). A total of 132 unique genes were annotated, including 86 protein coding genes, 38 tRNA genes, and 8 rRNA genes. Among these genes, 18 genes contained one or two introns. The overall GC contents of the plastid genome were 36.9%, and in the IR regions, LSC and SSC were 43.8, 34.4 and 30.9%, respectively. Maximum likelihood analysis revealed that the new sequenced species C. appendiculata was closer to the species in Cattleya and formed one clade with a high bootstrap value at the middle of the phylogenetic tree of Orchidaceae.

| S-EPMC7800390 | biostudies-literature

Next-generation sequencing of the complete mitochondrial genome of the Nixi chicken (Gallus gallus).

Project description:Nixi chicken is a type of Tibetan chickens who lives at high altitudes in China. In this study, we reported the first complete mitochondrial genome of Nixi chicken by using a next-generation sequencing method. The assembled complete mitogenome contains one control region, 2 ribosomal RNAs, 13 protein-coding genes and 22 transfer RNA genes. Our work provides a valuable source of data for the study of the evolution of the Gallus gallus mitochondrial genome and contributes to the Nixi chicken breeding improvement program.

| S-EPMC7781923 | biostudies-literature

Complete Genome Sequence of Southern tomato virus Identified in China Using Next-Generation Sequencing.

Project description:The complete genome sequence of Southern tomato virus (STV), a double-stranded RNA virus that affects tomato in China, was determined using small RNA deep sequencing. This Chinese isolate shares 99% sequence identity to other isolates from Mexico, France, Spain, and the United States. This is the first report of STV infecting tomatoes in Asia.

| S-EPMC4616180 | biostudies-literature

The complete mitochondrial genome of Hexagrammos agrammus (Scorpaeniformes: Hexagrammidae) by next-generation sequencing.

Project description:The complete mitochondrial genome of the Hexagrammos agrammus is presented in this study. The mitochondrial genome is 16,512 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition were similar to those of most other vertebrates. The nucleotide compositions of the heavy strand are 17.27% of G, 26.10% of T, 26.85% of A, and 29.78% 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 neighbour-joining (NJ) method showed that H. agrammus has the closer relationship with Hexagrammos otakii and Hexagrammos lagocephalus in the phylogenetic relationship.

| S-EPMC7782902 | biostudies-literature

Next-generation sequencing yields the complete mitochondrial genome of Microhyla beilunensis (Anura: Microhylidae).

Project description:The complete mitochondrial genome (mtDNA) of Microhyla beilunensis (Anura: Microhylidae) was sequenced and annotated. The length of mtDNA sequences of M. beilunensis was 16,721 bp, and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The overall nucleotide composition of this genome was 29.1% A, 24.5% C, 14.5% G, 31.9% T, with a total A + T content of 61%. Phylogenetic analysis using Bayesian Inference (BI) method revealed that M. beilunensis was closely related with other 8 species from the genus Microhyla. The mtDNA dataset could be utilized for studying the molecular ecology and population genetics of Microhylid frogs.

| S-EPMC7782835 | biostudies-literature

Complete mitochondrial genome of the three Colombian Caribbean loggerhead sea turtles, using next-generation sequencing.

Project description:The loggerhead turtle, Caretta caretta (Linnaeus, 1758), is an endangered sea turtle in Colombian Caribbean beach. In the present study was sequenced the complete mitochondrial DNA of three loggerhead turtles using Illumina next-generation sequencing (NGS). The average nucleotide frequency was A: 35% T: 26%, C: 27% and G: 12%. This genome provides knowledge to the study of genetic variations and evolution of mitochondrial genomes of C. caretta. The sequences were deposited at the GenBank database under the accession number MF554690.1, MF579504.1 and MF579505.1.

| S-EPMC7800953 | biostudies-literature

Next-generation sequencing yields the complete mitochondrial genome of Pterygoplichthys pardalis (Loricariidae; Siluriformes).

Project description:In this study, we report the complete mitochondrial genome of Pterygoplichthys pardalis has derived by next-generation sequencing. The complete mitochondrial genome of P. pardalis contains 16,425 bp encompassing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The base composition is A 31.79%, C 26.89%, G 14.63%, and T 26.69%, and its gene arrangement is consistent with mitochondrial genomes derived from other representatives of Loricariidae. A phylogenetic tree of 24 Loricariidae species constructed based on the 13 coding genes shows that P. pardalis is clustered with other Pterygoplichthys genus. It suggests that the molecular classification results confirm its external morphological characteristics. These results have reference value for the further study of phylogenetic relationship, taxonomic classification, and phylogeography of Loricariidae.

| S-EPMC8530479 | biostudies-literature