Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mitochondrial genome of Diachrysia nadeja (Lepidoptera: Noctuoidea: Noctuidae) and phylogenetic analysis.

ABSTRACT: Diachrysia nadeja is a polyphagous herbivorous moth within the family Noctuidae. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of D. nadeja. This mitogenome was 15,242 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA unit genes (rRNAs). Gene order was conserved and identical to most other previously sequenced Noctuidae. Except for cox1 started with CGA, all other PCGs started with the standard ATN codons. Most of the PCGs terminated with the stop codon TAA, whereas cox1, cox2, and nad4 end with the incomplete codon T-. The whole mitogenome exhibited heavy AT nucleotide bias (80.5%). Phylogenetic analysis showed that D. nadeja got together with three Ctenoplusia species (C. agnata, C. limbirena, and C. albostriata) with high support value, indicating Diachrysia had a closer relationship with Ctenoplusia within Noctuidae.

SUBMITTER: Gao S

PROVIDER: S-EPMC7889200 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of Dysgonia stuposa (Lepidoptera: Erebidae) and phylogenetic relationships within Noctuoidea.

Project description:To determine the Dysgonia stuposa mitochondrial genome (mitogenome) structure and to clarify its phylogenetic position, the entire mitogenome of D. stuposa was sequenced and annotated. The D. stuposa mitogenome is 15,721 bp in size and contains 37 genes (protein-coding genes, transfer RNA genes, ribosomal RNA genes) usually found in lepidopteran mitogenomes. The newly sequenced mitogenome contained some common features reported in other Erebidae species, e.g., an A+T biased nucleotide composition and a non-canonical start codon for cox1 (CGA). Like other insect mitogenomes, the D. stuposa mitogenome had a conserved sequence 'ATACTAA' in an intergenic spacer between trnS2 and nad1, and a motif 'ATAGA' followed by a 20 bp poly-T stretch in the A+T rich region. Phylogenetic analyses supported D. stuposa as part of the Erebidae family and reconfirmed the monophyly of the subfamilies Arctiinae, Catocalinae and Lymantriinae within Erebidae.

| S-EPMC7081777 | biostudies-literature

Characterization and phylogenetic analysis of the mitochondrial genome of Macdunnoughia hybrida (Lepidoptera: Noctuidae: Plusiinae).

Project description:Macdunnoughia hybrida is a polyphagous herbivorous moth within the family Noctuidae. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of M. hybrida. This mitogenome was 15,382 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). Except for cox1 started with CGA, all other PCGs started with the standard ATN codons. Most of the PCGs terminated with the stop codon TAA, whereas cox1, cox2 and nad4 end with the incomplete codon T--. The whole mitogenome exhibited heavy AT nucleotide bias (80.7%). Gene order was conserved and identical to most other previously sequenced Noctuidae. Phylogenetic analysis positioned M. hybrida in a well-supported clade with Diachrysia nadeja and three Ctenoplusia species. The relationships (Catocalinae + (Plusiinae + (Acronictinae + (Heliothinae + (Amphipyrinae + (Hadeninae + Noctuinae)))))) were supported within Noctuidae.

| S-EPMC8284135 | biostudies-literature

Characterisation and phylogenetic analysis of the complete mitochondrial genome of Ctenoplusia albostriata (Lepidoptera: Noctuidae: Plusiinae).

Project description:Ctenoplusia albostriata is a pest of composite plants such as Calendula officinalis L. and Dahlia pinnata. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of C. albostriata. This mitogenome was 15,284 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA unit genes (rRNAs). Gene order was conserved and was found to be identical to most other previously sequenced Noctuidae. The whole mitogenome exhibited heavy AT nucleotide bias (80.9%). Except for cox1 started with CGA, all other PCGs started with the standard ATN codons. Most of the PCGs terminated with the stop codon TAA, whereas cox1, cox2 and nad4 end with the incomplete codon T--. Phylogenetic analysis showed that the mitogenome of C. albostriata was similar to C. agnata and C. limbirena, and the subfamily Plusiinae was close to Acronictinae, Heliothinae, Amphipyrinae, Noctuinae, and Hadeninae.

| S-EPMC7707265 | biostudies-literature

The complete mitochondrial genome of Paragabara curvicornuta (Lepidoptera: Noctuoidea: Eribidae).

Project description:In this study, the complete mitochondrial genome (mitogenome) of Paragabara curvicornuta was sequenced for the first time by traditional PCR amplification and primer walking methods. As a circular DNA molecule, the entire mitogenome is 15,532 bp in length (GeneBank accession no. KT362742), and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an AT-rich region. The nucleotide composition is A (39.9%), C (12.0%), G (7.6%), and T (40.4%). Based onthe amino acid sequences of 13 PCGs from 43 noctuoid species as ingroups and two drepanoid species as outgroups, the phylogenetic trees was constructed. The phylogenetic relationships of the families among Noctuoidea are (Notodontidae, (Erebidae, (Nolidae, Noctuidae)). However, the phylogenetic position of P. curvicornuta is still unclear in the family Erebidae that is a monophyletic clade strongly supported by the bootstrap value of 100%.

| S-EPMC7800408 | biostudies-literature

Complete mitochondrial genome sequence of fruit-piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea).

Project description:The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides. All tRNAs have putative secondary structures that are characteristic of mitochondrial tRNA. Most of the PCGs were initiated by typical ATN codons. Five genes were initiated by unusual codons. Cox1 gene was initiated by an unusual CGA codon and terminated by the typical stop codon GAA. Six genes ended with a single T. The A + T-rich region of 336 bp consisted of repetitive sequences, including two ATAGA motifs, a 19 bp poly-T stretch and three microsatellite-like regions ((TA)4, (TA)6 and two (TA)7). Moreover, three large tandem (one 40 bp and two 25 bp) repeated elements were identified in A + T-rich region. Phylogenetic analysis using PCGs revealed that Superfamily Noctuoidea is a monophyletic group.

| S-EPMC5633087 | biostudies-literature

First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera.

Project description:The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (T?C) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.

| S-EPMC6795624 | biostudies-literature

Complete mitochondrial genome of Spodoptera littoralis (Lepidoptera: Noctuidae) from Egypt.

Project description:The polyphagous cotton leafworm (Spodoptera littoralis) is one of the most destructive herbivorous insects worldwide. The present study reports the complete mitochondrial genome of S. littoralis collected from Egypt. The circular-mapping mitogenome was 15,408 bp in length with an overall A + T content of 81.1%, encoding a common set of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. Most PCGs were found to use conventional ATN as the start codon and TAN as the stop codon. The phylogenetic tree based on the nucleic acid sequences of 13 shared PCGs of 29 Noctuidae species revealed that S. littoralis and Spodoptera litura are sister species. The data in this study will be helpful to understand geographical genetic variations, phylogenetic relationships, and species identification of S. littoralis.

| S-EPMC7872533 | biostudies-literature

The mitochondrial genome of the western bean cutworm, Striacosta albicosta (Lepidoptera: Noctuidae).

Project description:The complete 15,553?bp mitochondrial genome of the western bean cutworm, Stricosta albicosta, (Lepidoptera: Noctuidae) was assembled from paired end Illumina HiSeq2500 read data. Annotation showed 13 predicted protein coding genes (PCGs), 22 tRNAs and 2 rRNAs have an order and orientation typical of insect mitochondrial genomes, and the derived rearrangement of tRNA-Met, -Ile and -Gln upstream of nad2 as in other Lepidoptera. A 79.3% A?+?T content resulted in a bias for codons with A or T in the 3rd position, and prevalence of synonymous substitutions suggest the effects of purifying selection on the mitochondrial genome sequence. Two microsatellite repeat motifs, (CA)10(AT)19 and (AT)12, are respectively located in intergenic spaces between tRNA-Glu and -Phe and tRNA-Leu and 16S rRNA. Mitochondrial phylogenomics was able to resolve sub-families within the Noctuidae, and suggest analogous analyses may be applicable across other lepidopteran Families.

| S-EPMC7799526 | biostudies-literature

The Complete Mitochondrial Genome of Brachmia macroscopa (Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis.

Project description:The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.

| S-EPMC4725263 | biostudies-literature

The complete mitochondrial genome of Appias albina (Lepidoptera: Pieridae) and phylogenetic analysis.

Project description:The complete mitochondrial genome of Appias albina (Lepidoptera: Pieridae) was firstly sequenced and characterized in our study. The total length of mitogenome is 15,193 bp and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 A + T-rich region. The overall nucleotide composition was 38.4% of A, 8.0% of G, 40.9% of T, and 12.4% of C. Phylogenetic tree was reconstructed using Bayesian Inference (BI) to validate the taxonomic status of A. albina, exhibiting the close relationship with Appias remedios.

| S-EPMC7748610 | 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