Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis.

ABSTRACT: More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

SUBMITTER: Yu T

PROVIDER: S-EPMC8396625 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of Two Complete Mitochondrial Genomes of Ledrinae (Hemiptera: Cicadellidae) and Phylogenetic Analysis.

Project description:Mitochondrial genomes are widely used for investigations into phylogeny, phylogeography, and population genetics. More than 70 mitogenomes have been sequenced for the diverse hemipteran superfamily Membracoidea, but only one partial and two complete mtgenomes mitochondrial genomes have been sequenced for the included subfamily Ledrinae. Here, the complete mitochondrial genomes (mitogenomes) of two additional Ledrinae species are newly sequenced and comparatively analyzed. Results show both mitogenomes are circular, double-stranded molecules, with lengths of 14,927 bp (Tituria sagittata) and 14,918 bp (Petalocephala chlorophana). The gene order of these two newly sequenced Ledrinae is highly conserved and typical of members of Membracoidea. Similar tandem repeats in the control region were discovered in Ledrinae. Among 13 protein-coding genes (PCGs) of reported Ledrinae mitogenomes, analyses of the sliding window, nucleotide diversity, and nonsynonymous substitution (Ka)/synonymous substitution (Ks) indicate atp8 is a comparatively fast-evolving gene, while cox1 is the slowest. Phylogenetic relationships were also reconstructed for the superfamily Membracoidea based on expanded sampling and gene data from GenBank. This study shows that all subfamilies (sensu lato) are recovered as monophyletic. In agreement with previous studies, these results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the two recognized families of treehoppers (Aetalionidae and Membracidae). Relationships within Ledrinae were recovered as (Ledra + (Petalocephala + Tituria)).

| S-EPMC7563726 | biostudies-literature

Characterization and phylogenetic analysis of the mitochondrial genome of Mileewa ponta (Hemiptera: Cicadellidae: Mileewinae).

Project description:The mitogenome of one Mileewinae species Mileewa ponta was sequenced and annotated according to close Cicadellidae species in this study. Annotation shows the mitogenome of M. ponta is 15999 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The A + T content in the mitogenome was 79.9%. Besides, we further constructed a Bayesian Inference phylogenetic tree among M. ponta, M. albovittata, M. margheritae and other Cicadellidae species. Each subfamily species clustered together, and M. ponta clustered with M. albovittata, M. margheritae. This mitogenome will contribute to the further systematics and evolution study of subfamily Mileewinae.

| S-EPMC7782179 | biostudies-literature

Characterization of Two Complete Mitochondrial Genomes of Atkinsoniella (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications.

Project description:The complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78.4%, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (CR). For all PCGs, a standard start ATN codon (ATT, ATG, or ATA) was found at the initiation site, except for ATP8, for which translation is initiated with a TTG codon. All PCGs terminate with a complete TAA or TAG stop codon, except for COX2, which terminates with an incomplete stop codon T. All tRNAs have the typical cloverleaf secondary structure, except for trnS, which has a reduced dihydrouridine arm. Furthermore, these phylogenetic analyses were reconstructed based on 13 PCGs and two rRNA genes of 73 mitochondrial genome sequences, with both the maximum likelihood (ML) and Bayesian inference (BI) methods. The obtained mitogenome sequences in this study will promote research into the classification, population genetics, and evolution of Cicadellinae insects in the future.

| S-EPMC8070250 | biostudies-literature

Characterization of the Complete Mitochondrial Genomes of Two Species with Preliminary Investigation on Phylogenetic Status of Zyginellini (Hemiptera: Cicadellidae: Typhlocybinae).

Project description:To explore the characteristics of mitogenomes and reveal phylogenetic relationships of the tribes of Zyginellini and Typhlocybini in Typhlocybinae, mitogenomes of two species of the Zyginellini, Parazyginella tiani and Limassolla sp., were sequenced. Mitogenomes of both species contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a large non-coding region (A + T-rich region). These characteristics are similar to other Membracoidea mitogenomes. All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA/G or with an incomplete T codon. All tRNAs have the typical clover-leaf structure, except trnS1 which has a reduced DHU arm and the acceptor stem of trnR is 5 or 6 bp in some species, an unusual feature here reported for the first time in Typhlocybinae. The A + T-rich region is highly variable in length and in numbers of tandem repeats present. Our analyses indicate that nad6 and atp6 exhibit higher evolutionary rates compared to other PCGs. Phylogenetic analyses by both maximum likelihood and Bayesian methods based on 13 protein-coding genes of 12 species of Typhlocybinae suggest that Zyginellini are paraphyletic with respect to Typhlocybini.

| S-EPMC7600600 | biostudies-literature

Characterization of the leafhopper mitogenome of Mileewa alara (Hemiptera: Cicadellidae: Mileewinae) and its phylogenetic analysis.

Project description:The mitogenome data of leafhopper species Mileewa alara was assembled and annotated in this study. The results shows that length of M. alara is 16020 bp, consist of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and one control region. The A + T content in the mitogenome was 77.9%. Phylogenetic analysis based on 13 PCGs of four Mileewa species and other 29 Cicadellidae species, each subfamily species well separated. And M. alara clustered with M. ponta. This study also raised mitogenome of Mileewa number in GenBank to four.

| S-EPMC8009127 | biostudies-literature

The complete mitochondrial genomes of two erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) with assessment of the phylogenetic status and relationships of tribes of Typhlocybinae.

Project description:The number and classification of tribes in the leafhopper subfamily Typhlocybinae are not yet fully clear, and molecular data has recently been used to help resolve the problem. In this study, the mitochondrial genomes of Mitjaevia shibingensis Chen, Song & Webb, 2020 and M. dworakowskae Chen, Song & Webb, 2020 of the tribe Erythroneurini (Cicadellidae, Typhlocybinae) were sequenced. Most protein-coding genes (PCGs) start with ATN and end with TAA or TAG, and the AT content of these three codons were found differ from previous results that show that the first codon has the highest incidence. Two rRNA genes are highly conserved, and the AT content in 16S is higher than that of 12S. The nucleotide diversity and genetic distance among 13 PCGs of the four tribes from Typhlocybinae show that Empoascini nucleotide diversity is significantly less than in the other three tribes, and have the largest distance from the others, while Typhlocybini and Zyginellini have the smallest distance, indicating that the relationship between the two is the closest. The nad2, nad4, nad4L, and nad5 genes have greater nucleotide diversity, showing potential for use as the main markers for species identification. The phylogenetic analysis yielded a well-supported topology with most branches receiving maximum support and a few branches pertaining to relationships within Zyginellini and Typhlocybini receiving lower support. The species of these two tribes are intertwined, and it was impossible to resolve them into separate branches. In addition, the tribes Empoascini and Erythroneurini were recovered as monophyletic, and Alebrini was placed at the base of the tree as the most primitive. These results are broadly in line with other molecular phylogenetical studies which differ from traditional morphological classification.

| S-EPMC8144164 | biostudies-literature

Complete mitochondrial genome of Mukaria splendida Distant (Hemiptera: Cicadellidae: Deltocephalinae: Mukariini) and phylogenetic analysis.

Project description:The complete mitochondrial genome (mitogenome) of Mukaria splendida Distant, 1908 (Hemiptera: Cicadellidae: Deltocephalinae) was first reported in Mukariini. The length of this mitogenome is 16,711 bp, which has an A + T content of 79% (A = 44.5%, T = 34.5%, G = 8.8%, C = 12.2%). A total of 37 genes were annotated [13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and 2 ribosomal RNA genes (rRNA)]. Among the 37 genes, 4 protein coding genes (ND1, ND4, ND4L, ND5), 8 tRNA genes (trnQ, trnC, trnY, trnF, trnH, trnP, trnL2, trnV), and 2 rRNA (12S rRNA, 16S rRNA) were encoded by N chain, and the remaining genes were encoded by J chain. Overall, there were 14 gene overlaps and 9 gene gaps in the mitochondrial genome of this species. All PCGs were started with ATD (ATA/ATT/ATG), and stopped with TAR, except ATP6, which ends with single T. The phylogenetic analysis confirms that M. splendida clustered with other Deltocephalinae species.

| S-EPMC7894459 | biostudies-literature

The mitogenome of Mileewa margheritae (Hemiptera: Cicadellidae: Mileewinae).

Project description:In this study, the mitochondrial genome of Mileewa margheritae (Hemiptera: Cicadellidae: Mileewinae) was sequenced and annotated. The mitogenome of M. margheritae is 15376 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The A + T content in the mitogenome was 79%. Most of PCGs started with ATN and stopped with TAA while ATP8 and ND5 started with TTG, COX2, ND1 stopped with incomplete T, Cytb stopped with TAG. We further constructed a Bayesian phylogenetic tree among M. margheritae, M. albovittata and other Cicadellidae species. The constructed phylogenetic tree suggests the close evolutionary relationship between M. margheritae and M. albovittata.

| S-EPMC7782090 | 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 Bothrogonia qiongana (Hemiptera: Cicadellidae) with phylogenetic analyses.

Project description:The species of Bothrogonia qiongana was reported by Yang and Li in 1980. The mitogenome is 15,788 bp in length, including 37 genes and a control region, with an overall A + T content of 76.9%. Most of the PCGs start with ATN (ATA, ATC, ATT, ATG), but ND5 starts with TTG. All PCGs used TAA or TAG as stop codon except COX2 which is using incomplete single T--. The phylogenetic tree was reconstructed based on B. qiongana and 24 reference species, which is consistent with traditional taxonomy.

| S-EPMC7781934 | 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