Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The first mitochondrial genome from the Sterrhinae (Lepidoptera: Geometridae) and its phylogenetic implications.

ABSTRACT: In this study, the complete mitochondrial genome of a geometrid species, Idaea simplicior (Prout), was sequenced. The I. simplicior mitogenome is a circular, double-stranded molecule, with 15,950 bp in size. The typical 37 mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an A + T-rich region are included. Gene content and arrangement are highly conserved and typical of Lepidoptera. Interestingly, the I. simplicior mitogenome is rich in microsatellite sequences of (TA)_12-18 with a scattered distribution in six intergenic regions. Phylogenetic analyses based on the combined 37 mitochondrial genes show that the Larentiinae and Ennominae are monophyletic. The Sterrhinae, which is represented by the only I. simplicior sequenced in this study, shows a closer relationship with the Larentiinae than Ennominae, which confirms previous morphological studies.

SUBMITTER: Song L

PROVIDER: S-EPMC7748674 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The first mitochondrial genome from the Sterrhinae (Lepidoptera: Geometridae) and its phylogenetic implications.

Song Lu L Shi Yu-Xia YX Li Jun-Hao JH Su Si-Lin SL Zhang Hong-Fei HF Ding Wei-Li WL Yang Ming-Sheng MS

Mitochondrial DNA. Part B, Resources 20191212 1

In this study, the complete mitochondrial genome of a geometrid species, Idaea simplicior (Prout), was sequenced. The I. simplicior mitogenome is a circular, double-stranded molecule, with 15,950 bp in size. The typical 37 mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an A + T-rich region are included. Gene content and arrangement are highly conserved and typical of Lepidoptera. Interestingly, the I. simplicior mitogenome is rich in microsatellite sequences of (TA ...[more]

PMID: 33366492

Similar Datasets

Complete mitochondrial genome of the Pasiphila chloerata (Lepidoptera: Geometridae) and its phylogenetic implications.

Project description:In this study, the complete mitochondrial genome of Pasiphila chloerata (Mabille) was sequenced and its phylogenetic implications were investigated. The P. chloerata mitogenome is a circular, double-stranded molecule, with 15,602 bp in length. The typical 37 mitochondrial genes (13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) and an A + T-rich region are included. Gene content and arrangement are highly conserved and typical of Lepidoptera. Phylogenetic analyses based on the combined 37 mitochondrial genes consistently recovered the Larentiinae and Ennominae involved are reciprocally monophyletic with the highest supports. The P. chloerata was clustered with other two members of the Larentiinae, reinforcing that of previous morphological studies.

| S-EPMC7707744 | biostudies-literature

Characterization and phylogenetic analysis of the mitochondrial genome of xanthabraxas hemionata (lepidoptera: Geometridae).

Project description:Xanthabraxas hemionata (Guenée, 1858) is a medium-sized and slender-bodied forest pest in China. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of X. hemionata. This mitogenome was 15,309 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The gene order was conserved and identical to that of most other previously sequenced Geometridae species. Most of the PCGs of X. hemionata, except for cox1, have the conventional ATN start codon. Except for four genes (cox1, cox2, nad5, and nad4) that end with the incomplete stop codon T-, all other PCGs terminated with the stop codon TAA. Phylogenetic analysis positioned X. hemionata in a well-supported clade with the other Ennominae species. The relationships (Ennominae + (Sterrhinae + Larentiinae)) were supported by Geometridae.

| S-EPMC9387340 | biostudies-literature

Phylogenetic relationship and characterization of the complete mitochondrial genome of Milionia basalis (Lepidoptera: Geometridae).

Project description:Larvae of the geometrid moth Milionia basalis feed exclusively on the podocarp tree, Podocarpus macrophyllus. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of M. basalis. This mitogenome was 15,901 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). The whole mitogenome exhibited heavy AT nucleotide bias (82.2%). Gene order was conserved and identical to most other previously sequenced Geometridae. Most PCGs of M. basalis had the conventional start codons ATN, with the exception of nad1 (TTG) and cox1 (CGA). Except for four genes (cox1, cox2, nad5, and nad4) end with the incomplete stop codon T--, all other PCGs terminated with the stop codon TAA. Phylogenetic analysis showed that M. basalis got together with Apocheima cinerarius, Jankowskia athlete, and four Biston species (B. panterinaria, B. perclara, B. suppressaria, and B. thibetaria).

| S-EPMC7707798 | 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 (TψC) 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

The mitochondrial genome of Erannis ankeraria (Lepidoptera: Geometridae).

Project description:The measuring worm Erannis ankeraria belongs to the subfamily Ennominae of Geometridae. The mitogenome (GenBank accession number: MN046105) of E. ankeraria was sequenced, the new representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,250 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Geometridae. The nucleotide composition biases towards A and T, which together made up 79.3% of the entirety. Bayesian inference analysis strongly supported the monophyly of Bombycoidea, Geometroidea, Noctuoidea, Papilionoidea, Pyraloidea, and Tortricoidea were strongly supported. This result also suggested that the Geometroidea was the sister to Bombycoidea, and then Noctuoidea was assigned to the sister group to the clade of Geometroidea + Bombycoidea, and then Pyraloidea was the sister group to the clade that contains Geometroidea, Bombycoidea, and Noctuoidea, and then Papilionoidea was the sister group to the clade that contains these four superfamilies mentioned above.

| S-EPMC7706540 | biostudies-literature

Complete mitochondrial genome of Biston thoracicaria (Lepidoptera: Geometridae).

Project description:The complete mitochondrial genome (mitogenome) of Biston thoracicaria (Lepidoptera: Geometridae) is 15,538 bp in length, containing 13 PCGs, 22 tRNAs, two rRNAs, and an A + T-rich region. All PCGs initiate with typical start codon of ATN and share the complete stop codon of TAA, whereas cox1 starts with CGA. The ML analysis was performed using a dataset matrix containing 13 PCGs concatenated from the mitogenomes of Geometridae species. Our study presented the phylogenetic relationship of (Larentiinae + ((Sterrhinae + (Ennominae + Geometrinae))). Within the genera Biston, B. thoracicaria grouped with other species as the sister group.

| S-EPMC8216253 | biostudies-literature

The complete mitochondrial genome of a jujube geometrid, Sucra jujuba (Lepidoptera: Geometridae) and its phylogenetic analysis.

Project description:Sucra jujuba Chu, 1979 (Lepidoptera: Geometridae) is a major insect pest in jujube plantation. In this study, we have sequenced the complete mitochondrial genome of S. jujuba. The circular genome was 15,557 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one AT-rich region (GenBank accession no. MZ507574). The nucleotide composition was significantly biased (A, T, C, and G were 41.85%, 39.65%, 10.97%, and 7.53%, respectively) with A + T contents of 81.50%. The Bayesian phylogenetic analysis of the concatenated nucleotide sequences of 13 PCGs from 30 species in the subfamily Ennominae and two outgroup species was performed. The results indicated that S. jujuba was closely related to Amraica recursaria in the subfamily Ennominae.

| S-EPMC11198131 | biostudies-literature

The complete mitochondrial genome of Semiothisa cinerearia Bremer & Grey 1853 (Lepidoptera: Geometridae: Ennominae) and its phylogenetic analysis.

Project description:Semiothisa cinerearia Bremer & Grey, 1853 belongs to the lepidopteran family Geometridae, subfamily Ennominae. We sequenced the complete mitochondrial genome of S. cinerearia by PCR and Sanger sequencing method. The mitochondrial genome of S. cinerearia is 15,523 bp in length and contains a typical set of 37 genes with 'MIQ' type gene arrangement and a 394 bp AT-rich regions. Except for cox1 using CGA as initiation codon, all protein-coding genes (PCGs) start with ATN codons and except for nad2 and nad4l using TAG as termination codon, all PCGs terminated with TAA codon. A phylogenetic tree including 39 genus of subfamily Ennominae was first reconstructed based on the mitochondrial genome sequences with nucleotide substitution model GTR + G + I, which showed that the genera Amraica, Jankowskia, and Ectropis are not monophyletic and S. cinerearia and Macaria notata are classified together.

| S-EPMC10769541 | biostudies-literature

The complete mitochondrial genome of Chibiraga houshuaii (Lepidoptera, Limacodidae) and its phylogenetic implications.

Project description:Chibiraga is a mall East Asian genus in the family Limacodidae (slug-moths). The latter includes many agricultural pests. Mitochondrial genome analysis is an important tool for studying insect molecular identification and phylogenetics. However, there are very few mitogenome sequences available for Limacodidae species, and none for the genus Chibiraga at all. To explore the mitogenome features of Chibiraga and verify its phylogenetic position, the complete mitogenome of Chibiraga houshuaii was sequenced and annotated. The complete 15,487 bp genome encoded 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Most of the PCGs had typical ATN start codons and terminated with TAA or a single T residue. UUA (Leu2), AUU (Ile), UUU (Phe), AUA (Met) and AAU (Asn) were the five most frequently used codons. All tRNAs were folded into cloverleaf secondary structure, except for trnS1, which lacked the DHU arm. Phylogenetic analyses within the superfamily Zygaenoidea were performed based on multiple datasets from mitochondrial genes. The results showed that the families Phaudidae, Limacodidae and Zygaenidae were respectively recovered as monophyly; C. houshuaii was clustered in a clade with nettle type larvae in Limacodidae.

| S-EPMC10963781 | biostudies-literature

Characterization of the complete mitochondrial genome of Ectropis grisescens (Lepidoptera, Geometridae).

Project description:Ectropis grisescens (Lepidoptera, Geometridae) is one of the main leaf-eating pests in tea plantations in China. In this study, the complete mitochondrial genome of this species was sequenced and assembled. The total length of the mitochondrial genome of E. grisescens was 15,794 bp (GenBank accession No. MW337302). The base composition was 41.26% for A, 39.49% for T, 7.92% for G, and 11.33% for C. The circular mitogenome contained 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis performed using 13 protein-coding genes of 15 species of Geometridae and an out-group Pieris melete (Lepidoptera, Pieridae) showed that E. grisescens is closely related to species of E. obliqua, and this is consistent with the morphological identification.

| S-EPMC8205040 | 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