Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete mitochondrial genome of Nemoura meniscata Li & yang (Plecoptera: Nemouridae) from China.

ABSTRACT: We sequenced the third complete mitochondrial genome of Nemoura meniscataby using the high-throughput sequencing method. The mitochondrial genome harbored 37 typical code genes and a control region with 15,895 bp in length was a double-stranded and circular genome. The nucleotide composition is partial to A and T. Seventy-eight nucleotides were dispersed in 10 intergenic spacers and gene overlaps were also found at 13 gene junctions with 48 nucleotides. In phylogenetic trees, the 13 Nemouridae species form a clade diverged from the outgroup clade. The genus Nemoura and Amphinemura were sister groups which is consistent with the previous study.

SUBMITTER: Chen S

PROVIDER: S-EPMC7748651 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete mitochondrial genome of Nemoura meniscata Li & yang (Plecoptera: Nemouridae) from China.

Chen Sijin S Cao Jinjun J Li Weihai W Wang Ying Y

Mitochondrial DNA. Part B, Resources 20200203 1

We sequenced the third complete mitochondrial genome of Nemoura meniscataby using the high-throughput sequencing method. The mitochondrial genome harbored 37 typical code genes and a control region with 15,895 bp in length was a double-stranded and circular genome. The nucleotide composition is partial to A and T. Seventy-eight nucleotides were dispersed in 10 intergenic spacers and gene overlaps were also found at 13 gene junctions with 48 nucleotides. In phylogenetic trees, the 13 Nemou ...[more]

PMID: 33366870

Similar Datasets

Complete Mitochondrial Genome of Malenka flexura (Plecoptera: Nemouridae) and Phylogenetic Analysis.

Project description:The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial genome (mitogenome) of Malenka flexura of the genus Malenka was firstly sequenced and analyzed. The phylogeny of Amphinemurinae was also reconstructed using 13 proteincoding genes (PCGs) from previously published stoneflies. This mitogenome was 15,744 bp long and encoded the typical 37 genes, as well as a putative control region. The gene arrangement of M. flexura mitogenome is identical with the putative ancestral mitogenome in Drosophila yakuba. Most PCGs used standard ATN as start codons and TAA/TAG as termination codons. All tRNA genes exhibited the typical cloverleaf secondary structure, except for tRNASer(AGN), whose dihydrouridine (DHU) arm was lacking. Some structural elements in the control region were founded, such as tandem repeat regions, stemloop structures, polyN stretch and microsatellite structure, etc. Phylogenetic analyses of sequenced Amphinemurinae mitogenomes unsupported the sister relationship of Amphinemura and Malenka. Finally, the phylogenetic analyses inferred a relationship within Amphinemurinae: Amphinemura + (Malenka + (Protonemura + (Indonemoura + (Sphaeronemoura + Mesonemoura)))).

| S-EPMC9142110 | biostudies-literature

The complete mitochondrial genome of a stonefly species, Indonemoura auriformis (Plecoptera: Nemouridae).

Project description:One new mitochondrial genome of Indonemoura auriformis from the family Nemouridae (Insecta: Plecoptera) was sequenced in the study. The mitochondrial genome has the length of 15,718 bp, encoding 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The whole nucleotide composition biased adenine and thymine with A + T accounting for 69.9%. Nine PCGs and 14 tRNA genes are encoded in the J chain, the other four PCGs, eight tRNAs, and two rRNA genes are encoded in the chain of N. The mitochondrial genome includes 13 gene overlaps and 12 intergenic spacers. Most PCGs strictly use the ATN as start codon, and terminate with traditional stop codon (TAA and TAG). Except the tRNASer(AGN) seems to lack dihydrogen glycine arm, all tRNA genes of the mitochondrial genome are the typical clover secondary structure. The phylogenetic tree of PCGs dataset based on bayesian inference (BI) and maximum likelihood (ML) analysis show the same tree topology. Both ML and BI analysis support the sister-group relationship between Amphinemuria and Nemoura. Meanwhile, Capniidae is closely related to Taeniopterygidae.

| S-EPMC7707255 | biostudies-literature

The complete mitochondrial genome of Amphinemura bulla Shimizu, 1997 (Plecoptera: Nemouridae) from Japan.

Project description:The genus Amphinemura belongs to the family Nemouridae (Plecoptera) and has 205 species in the Holarctic and Oriental Regions. We sequenced the fourth complete mitochondrial genome of A. bulla Shimizu, 1997. The mitogenome is 15,827 bp long with 37 genes plus a control region with an A + T content of 68.9%. There are 10 intergenic spacers (75 bp total) and 13 gene overlaps (43 bp total). All protein-coding genes (PCGs) use normal initiation codons, except ND1 and ND5 which begin with TTG and GTG. Two PCGs (COII and ND5) use a single T as a partial termination codon. Phylogenetic analyses showed that Nemoura and Amphinemura were sister group resulting in a paraphyletic Amphinemurinae different from the morphological classification.

| S-EPMC7971268 | biostudies-literature

The mitochondrial genome analysis of Sphaeronemoura elephas (Plecoptera: Nemouridae) from Jiangxi Province of southeastern China.

Project description:We sequenced and annotated the species of Sphaeronemoura elephas which represents the first record for continental China from Jiangxi Province in this study to provide mitochondrial genome data for future studies. The entire mitochondrial genome of S. elephas harbored 37 typical code genes and one control region with 15,846 bp in length. The A + T account of total nucleotide, PCGs, tRNAs, rRNAs and control region were 67.1, 64.5, 70.5, 71.0, 82.4%, respectively and the A + T content was the highest in control region. The start codon of all PCGs used ATN except ND5 and ND1 started with GTG and TTG. Eleven PCGs used typical terminal codon TAA or TAG while the COII and ND5 stopped with the single T. Based on 13 PCGs by using Bayesian (BI) and maximum-likelihood (ML) methods, we found that the genus Sphaeronemoura and Mesonemoura were sister groups and the species of Amphinemurinae was monophyletic group.

| S-EPMC7748612 | biostudies-literature

The mitochondrial genome analysis of a stonefly, Nemoura longicercia Okamoto, 1922 (Plecoptera: Nemouridae).

Project description:To better understand the diversity and phylogeny of Nemouridae, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Nemoura longicercia Okamoto, 1922. The entire mitochondrial genome of N. longicercia was 15,728 bp. It contained 37 representative genes (22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNA genes (rRNAs)) and a control region. In this genome, 23 genes were found on the heavy strand (H-strand) and 14 genes were on the light strand (L-strand). All PCGs began with the initiation codon ATN. Eleven PCGs stopped with the termination codon TAA or TAG, while COII and ND5 genes stopped with incomplete codon T. Bayesian's inference (BI) and maximum-likelihood (ML) methods generated the identical tree topology across the PCGR dataset (13 PCGs plus two rRNAs). The monophyly of each subfamily was well-supported. This analysis supported the clade N. longicercia plus N. papilla as sister taxon to the clade N. meniscata plus N. nankinensis.

| S-EPMC9621250 | biostudies-literature

Mitochondrial genomes of Nemourinae species (Plecoptera: Nemouridae) and the phylogenetic implications.

Project description:Currently, the classification system of 2 subfamilies within Nemouridae has been widely accepted. However, monophyly of 2 subfamilies has not been well supported by molecular evidence. To date, only mitogenomes from genus Nemoura of the subfamily Nemourinae were used in previous phylogenetic studies and produced conflicting results with morphological studies. Herein, we analyzed mitogenomes of 3 Nemourinae species to reveal their mitogenomic characteristics and to examine genus-level classification among Nemouridae. In this study, the genome organization of 3 mitogenomes is highly conserved in gene order, nucleotide composition, codon usage, and amino acid composition. In 3 Nemourinae species, there is a high variation in nucleotide diversity among the 13 protein-coding genes (PCGs). The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. The phylogenetic analyses highly support Nemurella as the sister group to Ostrocerca. Meanwhile, Nemoura is recovered as the sister group of Malenka; they are grouped with other Amphinemurinae and emerged from a paraphyletic Nemourinae. More molecular data from different taxonomic groups are needed to understand stoneflies phylogeny and evolution.

| S-EPMC10914373 | biostudies-literature

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications.

Project description:The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.

| S-EPMC5454909 | biostudies-literature

The first complete mitochondrial genome sequence of Cacopsylla citrisuga (Yang & Li), a new insect vector of Huanglongbing in Yunnan Province, China.

Project description:Cacopsylla citrisuga (Yang & Li) is an important pest-threatening Citrus and Poncirus plants (Rutaceae) and a newly identified insect vector of citrus Huanglongbing. The complete mitochondrial genome of C. citrisuga was 14,906 bp in length, with 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs). The phylogenetic trees inferred from Bayesian inference and maximum likelihood analyses confirmed C. citrisuga as a member of the genus Cacopsylla. Our phylogenetic analyses suggested that the Cacopsylla is paraphyletic, and confirmed C. citrisuga as a member of clade-I under Cacopsylla. The complete mitochondrial genome of C. citrisuga will provide important information for the phylogeny and evolution analysis of Cacopsylla.

| S-EPMC7889111 | biostudies-literature

Three new species of Illiesonemoura Baumann, 1975 (Plecoptera, Nemouridae) from China.

Project description:BackgroundThe genus Illiesonemoura Baumann, 1975 (Plecoptera, Nemouridae) is a small-sized stonefly with slender and curved embranous cerci. Currently, 18 species of the genus are known worldwide, mainly distributed in the Palaearctic and Oriental Regions, with a total of two species known to China.New informationThree new species of Illiesonemoura Baumann, 1975, I.bituberculata Wang & Du, sp. nov., I.motuoensis Du & Ji, sp. nov. and I.weii Du & Ji, sp. nov. are described and illustrated, based on male adults from China. Illiesonemourabituberculata is characterised by two pairs of tubercles arising posteromedially from tergum 10 and by two rows of spinules outlining the lateral edge of the ventral sclerite of the epiproct. Illiesonemouramotuoensis is characterised by the heart-shaped epiproct with a thin and slightly sclerotised protrusion between the sclerotised bands. Illiesonemouraweii is characterised by a pair of small knobs on tergum 10, outer lobes of paraprocts basally broad, then slender towards apices with a pointed tip and the epiproct with lateral spinules.

| S-EPMC10838080 | biostudies-literature

Two new species of the stonefly genus Amphinemura (Insecta, Plecoptera, Nemouridae) from China.

Project description:Two new species of the genus Amphinemura Ris from China are described and illustrated, i.e. A. annulata Du & Ji, sp. n. from Zhejiang, Shanxi, Shaanxi and Guizhou Province, and A. lingulata Du & Wang, sp. n. from Shaanxi and Sichuan Province. A. annulata is similar to A. tricintusidens Wang & Zhu in having an apical cavity of the epiproct, but the epiproct ventral sclerite and the median paraproct lobe of the two species are different. A. lingulata is related to A. didyma Zhu & Yang in having the similar epiproct, but they differ mostly in paraproct median and outer lobes.

| S-EPMC4023258 | biostudies-literature