Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Pentatoma rufipes (Hemiptera, Pentatomidae) and its phylogenetic implications.

ABSTRACT: Pentatoma rufipes (Linnaeus, 1758) is an important agroforestry pest widely distributed in the Palaearctic region. In this study, we sequence and annotate the complete mitochondrial genome of P. rufipes and reconstruct the phylogenetic trees for Pentatomoidea using existing data for eight families published in the National Center for Biotechnology Information database. The mitogenome of P. rufipes is 15,887-bp-long, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region, with an A+T content of 77.7%. The genome structure, gene order, nucleotide composition, and codon usage of the mitogenome of P. rufipes were consistent with those of typical Hemiptera insects. Among the protein-coding genes of Pentatomoidea, the evolutionary rate of ATP8 was the fastest, and COX1 was found to be the most conservative gene in the superfamily. Substitution saturation assessment indicated that neither transition nor transversion substitutions were saturated in the analyzed datasets. Phylogenetic analysis using the Bayesian inference method showed that P. rufipes belonged to Pentatomidae. The node support values based on the dataset concatenated from protein-coding and RNA genes were the highest. Our results enrich the mitochondrial genome database of Pentatomoidea and provide a reference for further studies of phylogenetic systematics.

SUBMITTER: Zhao L

PROVIDER: S-EPMC8206063 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete mitochondrial genome and phylogenetic implications for Eurydema maracandica (Hemiptera: Pentatomidae).

Project description:The complete mitochondrial genome of Eurydema maracandica was sequenced and was 15,391 bp long with 76.82% A + T. There were 37 typical genes including 13 protein-coding genes/PCGs, 22 transfer RNA/tRNAs, and 2 ribosomal RNA/rRNAs. The 690 bp D-loop region was located between 12S rRNA and trnI-Ile. All PCGs started with ATN codons, except COI, ATP8, and ND1, and ended with TAA, except COI, COII, and ND5. Phylogenetic analyses indicated highly supported monophyly for each family, and Pentatomidae species formed a solid monophyletic group. Eurydema maracandica and Eurydema gebleri were clustered sibling clades, and the genus Halyomorpha was close to Eurydema.

| S-EPMC7800374 | biostudies-literature

The complete mitochondrial genome of Palomena viridissima (Hemiptera: Pentatomidae) and phylogenetic analysis.

Project description:Here, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Palomena viridissima (Hemiptera: Pentatomidae). This mitogenome was 15,118 bp long, comprising of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rrnL and rrnS) and a large non-coding control region. The P. viridissima mitogenome with an A + T content of 76.0%, presented a positive AT-skew (0.11) and a negative GC-skew (-0.13). Ten PCGs started with a typical ATN codon, two PCGs started with TTG (atp8, nad1), whereas the remaining one used AAC (cox1). All tRNAs had a typical secondary cloverleaf structure, except for trnS1 which lacked the dihydrouridine arm. The Bayesian phylogenetic analysis based on mitogenomic data supported a sister relationship of P. viridissima and Nezara viridula from the same tribe Nezarini and recovered a phylogeny of Pentatominae: (Menidini + (Strachiini + (Pentatomini + ((Cappaeini + Halyini) + (Eysarcorini + (Nezarini + Carpocori)))))).

| S-EPMC8043517 | biostudies-literature

The first mitochondrial genome for the subfamily Podopinae (Hemiptera: Pentatomidae) and its phylogenetic implications.

Project description:Here, we determined the complete mitogenome of Graphosoma rubrolineata, as the first representative for the subfamily Podopinae. This mitogenome is 15,633 bp long and contains 37 typical mitochondrial genes. The genome size, gene arrangement, A + T content, codon usage and secondary structures of 22 tRNAs of the G. rubrolineata mitogenome were similar to that of other sequenced pentatomoids. This mitogenome exhibited a reverse nucleotide strand bias, i.e. positive GC-skew (0.021) and negative AT-skew (-0.086). Phylogenetic analyses based on mitogenomic data strongly supported the monophyly of each of the five superfamilies within Pentatomomorpha and recognized a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))). However, G. rubrolineata clustered with three Pentatominae species, suggesting that Pentatominae probably was not monophyletic, or Podopinae may not be a valid taxonomic group. The mitogenome sequence of G. rubrolineata could contribute for better understanding of population genetics and evolution of this insect pest.

| S-EPMC7800415 | biostudies-literature

Complete Mitochondrial Genome of Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) and Phylogenetic Analysis of Pentatomomorpha Species.

Project description:Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) is used as a biological control agent against various insect pests for its predatory. In the present study, the complete mitochondrial genome (mitogenome) of the species was sequenced using the next-generation sequencing technology. The results showed that the mitogenome is 15,952 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. Furthermore, the gene order and orientation of this mitogenome are identical to those of most heteropterans. There are 21 intergenic spacers (of length 1-28 bp) and 13 overlapping regions (of length 1-23 bp) throughout the genome. The control region is 1,291 bp long. The start codon of the PCGs is ATN, except cox1 (TTG), and stop codon is TAA, except nad1 (TAG). The 22 tRNAs exhibit a typical cloverleaf secondary structure, except trnS1, which lacks a dihydrouridine (DHU) arm and trnV, where the DHU arm forms a simple loop. The analyses based on nucleotide sequences of the 13 PCGs by Bayesian Inference and maximum likelihood methods. The results support the monophyly of five superfamilies Aradoidea, Pentatomoidea, Pyrrhocoroidea, Lygaeoidea, and Coreoidea. Within Pentatomoidea, the relationship observed is as follows: (Plataspidae + Urostylididae) + (Pentatomidae + (Acanthosomatidae + (Cydnidae + (Scutelleridae + (Dinidoridae + Tessaratomidae))))), and D. dybowskyi was placed in Pentatomidae and close to Eurydema gebleri.

| S-EPMC5905379 | biostudies-literature

The complete mitochondrial genome of Plautia crossota (Hemiptera: Pentatomidae).

Project description:In this study, we elucidated the complete mitochondrial genome (mitogenome) of Plautia crossota. The circular mitogenome is 16,809 bp long, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The overall base composition is as follows: A, 41.6%; T, 32.75%; C, 14.84%; G, 10.81%; a slight A + T bias of 74.35%. Phylogenetic analysis of 20 species of Pentatomoidea revealed that Plautia crossota was closer to Nezara viridula.

| S-EPMC7687649 | biostudies-literature

Characterizing the Complete Mitochondrial Genome of Arma custos and Picromerus lewisi (Hemiptera: Pentatomidae: Asopinae) and Conducting Phylogenetic Analysis.

Project description:We characterized the mitochondrial genome (mitogenome) and conducted phylogenetic analyses of 48 Hemiptera species by sequencing and analyzing the mitogenome of Arma custos (Fabricius) and Picromerus lewisi (Scott). The complete mitogenomes of the two predators were 16,024 bp and 19,587 bp in length, respectively, and it contained 37 classical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), and a control region. Most PCGs in these predators use ATN as the start codon. This research revealed that the genes of the two natural enemy species have an A + T content of 75.40% and all tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. This is the first study to compare the mitochondrial genetic structure of two predatory insects; the mitochondrial genetic structure of individual predatory insects has been sequenced in previous studies. Here, phylogenetic analysis on the basis of amino acid and nucleotide sequences of 13 mitochondrial PCGs using Bayesian inference and maximum likelihood methods were conducted to generate similar tree topologies, which suggested that the two predators with close genetic relationships belong to Asopinae subfamily. Furthermore, the monophyly of the Pentatomoidea superfamily is well accepted despite limited taxon and species sampling. Finally, their complete mitogenome provided data to establish a predator-prey food web, which is the foundation of effective pest management. Our results also enhanced the database of natural enemy insects.

| S-EPMC8763613 | biostudies-literature

Characterization of the complete mitochondrial genome of Pentatoma semiannulata (Hemiptera: Pentatomidae).

Project description:The Pentatoma semiannulata is an important fruit pest in Chinese agricultural system. In current study, the complete mitochondrial genome of P. semiannulata is determined. This mitogenome is 15,515 bp in size and comprises of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Gene order is identical to that of the putative ancestral arrangement of insects. All protein-coding genes initiate with ATN, except for ATP8, COX1 and NAD1 use GTG or TTG as the start codon, and terminate with TAA with the exception for COX2 which uses a single T residue as the stop codon. All tRNAs, ranging from 62 to 72 bp, have the clover-leaf structure except for tRNASer(AGN) . The monophyly of Pentatomidae is highly supported by the phylogenetic tree and P. semiannulata is very close to other herbivorous species of the remaining Pentatomidae species.

| S-EPMC7954408 | biostudies-literature

The Complete Mitochondrial Genome of Four Hylicinae (Hemiptera: Cicadellidae): Structural Features and Phylogenetic Implications.

Project description:To reveal mtgenome characterizations and reconstruct phylogenetic relationships of Hylicinae, the complete mtgenomes of four hylicine species, including Nacolus tuberculatus, Hylica paradoxa, Balala fujiana, and Kalasha nativa, were sequenced and comparatively analyzed for the first time. We also carried out the richest (11) subfamily sampling of Cicadellidae to date, and reconstructed phylogenetic relationships of Membracoidea among 61 species based on three datasets using maximum likelihood and Bayesian inference analyses. All new sequenced mtgenomes are molecules ranging from 14,918 to 16,221 bp in length and are double stranded, circular in shape. The gene composition and arrangement of these mtgenomes are consistent with members of Membracoidea. Among 13 protein-coding genes, most show typical ATN start codons and TAR (TAA/TAG) or an incomplete stop codon T-, and several genes start by TTG/GTG. Results of the analysis for sliding window, nucleotide diversity, and nonsynonymous substitution/synonymous substitution indicate cox1 is a comparatively slower-evolving gene while atp8 is the fastest gene. In line with previous researches, phylogenetic results indicate that treehopper families are paraphyletic with respect to family Cicadellidae and also support the monophyly of all involved subfamilies including Hylicinae. Relationships among the four hylicine genera were recovered as (Hylica + (Nacolus + (Balala + Kalasha))).

| S-EPMC7762291 | biostudies-literature

The complete mitochondrial genome of the stink bug Eocanthecona furcellata (Hemiptera: Pentatomidae).

Project description:The predatory stink bug Eocanthecona furcellata belongs to the subfamily Asopinae of Pentatomidae. In the current study, the complete mitochondrial genome of E. furcellata is determined. This mitogenome is 16,085 bp in size and comprises of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Gene order is identical to that of the putative ancestral arrangement of insects. Nucleotide composition is biased toward A and T, which together made up 75.5% of the entire genome. All tRNAs have the clover-leaf structure except for the tRNASer(AGN) and the length of them ranges from 61 to 73 bp. The monophyly of Pentatomidae is highly supported by the phylogenetic tree and E. furcellata is very close to other carnivorous species of the remaining Pentatomidae species.

| S-EPMC8477922 | biostudies-literature

First complete mitochondrial genome of the tribe Coccini (Hemiptera, Coccomorpha, Coccidae) and its phylogenetic implications.

Project description:Soft scale insects (Hemiptera, Coccidae) are important pests of various agricultural and horticultural crops and ornamental plants. They have negative impacts on agriculture and forestry. The tribe Coccini represents one of the most ancient evolutionary lineages of soft scale insects. However, no complete Coccini mitochondrial genome (mitogenome) is available in public databases. Here, we described the complete mitogenome of Coccushesperidum L., 1758. The 15,566 bp mitogenome of C.hesperidum had a high A+T content (83.4%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Only seven tRNAs had the typical clover-leaf secondary structure and the remaining tRNAs lacked the DHU arm, TψC arm or both. Moreover, a comparative analysis of all reported scale insect mitogenomes from GenBank database was performed. The mitogenomes of scale insects showed high similarities in base composition and A+T content. Additionally, our phylogenetic analysis confirmed the monophyly of Coccomorpha and revealed that the archaeococcoids were the most basal lineage within Coccomorpha, while Ericeruspela and Didesmococcuskoreanus, belonging to Coccidae, were often mixed with Aclerdidae, making Coccidae a paraphyletic group. These findings expand the mitogenome database of scale insects and provide new insights on mitogenome evolution for future studies across different insect groups.

| S-EPMC10838174 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data