scholarly journals The complete mitochondrial genomes of two weevils, Eucryptorrhynchus chinensis and E. brandti: conserved genome arrangement in Curculionidae and deficiency of tRNA-Ile gene

2016 ◽  
Vol 11 (1) ◽  
pp. 458-469 ◽  
Author(s):  
Zhen-Kai Liu ◽  
Peng Gao ◽  
Muhammad Aqeel Ashraf ◽  
Jun-Bao Wen
Keyword(s):  
Tandem Repeats ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Rich Region ◽  
Illumina Hiseq ◽  
Ancestral Gene ◽  
Complete Sequences ◽  
Genome Arrangement ◽  
Reading Frames ◽  
Complete Mitochondrial Genomes

AbstractThe weevils Eucryptorrhynchus chinensis and Eucryptorrhynchus brandti (Coleoptera: Curculionidae), are two of the most important pests of the tree-of-heaven, Ailanthus altissima, which is found throughout China. In this study, the complete mitogenomes of the two weevils have been sequenced using Illumina HiSeqTM 2000. The mitogenomes of E. chinensis and E. brandti are 15,628bp and 15,597bp long with A+T contents of 77.7% and 76.6%, respectively. Both species have typical circular mitochondrial genomes that encode 36 genes. Except the deficiency of tRNA-Ile, the gene composition and order of E. chinensis and E. brandti are identical to the inferred ancestral gene arrangement of insects. In both mitochondrial genomes, the start codons for COI and ND1 are AAT and TTG, respectively. A5bp motif (TACTA) is detected in intergenic region between the tRNA-Ser (UCN) and ND1 genes. The ATP8/ATP6 and ND4L/ND4 gene pairs appear to overlap four or seven nucleotides (ATAA/ATGATAA) in different reading frames. The complete sequences of AT-rich region have two regions including tandem repeats. The study identifies useful genetic markers for studying the population genetics, molecular identification and phylogeographics of Eucryptorrhynchus weevils. The features of the mitochondrial genomes are expected to be valuable in

scholarly journals Characterization of the Complete Mitochondrial Genomes from Two Nitidulid Pests with Phylogenetic Implications

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 779
Author(s):  
Xiaoxiao Chen ◽  
Qing Song ◽  
Min Huang
Keyword(s):  
Tandem Repeats ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Start Codon ◽  
Mitochondrial Genomes ◽  
Sister Group Relationship ◽  
Rich Region ◽  
Phylogenetic Implications ◽  
Complete Mitochondrial Genomes

The complete mitochondrial genomes of Xenostrongylusvariegatus and Epuraea sp. were sequenced and analyzed. The total genome lengths are 17,657 and 16,641 bp, with an A+T content of 77.2% and 76.4%, respectively. Each mitochondrial genome consists of 37 coding genes and a non-coding (AT-rich) region. All protein-coding genes (PCGs) start with the standard start codon, ATN, and end with complete stop codons, TAA and TAG, or an incomplete stop codon, T. All tRNAs can be folded into the typical clover-leaf secondary structure, with the exception of trnS1 in both species with a reduced dihydrouridine (DHU) arm. The AT-rich region has tandem repeats differing in both number and length. Genetic distance and Ka/Ks analyses show that nad6 has a higher variability and more rapid evolutionary rate than other PCGs. Both maximum likelihood and Bayesian inference phylogenetic analyses based on 13 PCGs and 2 ribosome DNAs (rDNAs) agree with the previous phylogenies in supporting the Nitidulidae monophyly and the sister-group relationship of Kateretidae + (Monotomidae + Nitidulidae).

scholarly journals Mitochondrial genomes of the stoneflies Mesonemoura metafiligera and Mesonemoura tritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea

ZooKeys ◽  
2019 ◽  
Vol 835 ◽  
pp. 43-63 ◽  
Author(s):  
Jin–Jun Cao ◽  
Ying Wang ◽  
Yao–Rui Huang ◽  
Wei–Hai Li
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Rich Region ◽  
Stem Loop ◽  
Protein Coding ◽  
The Family

In this study, two new mitochondrial genomes (mitogenomes) ofMesonemourametafiligeraandMesonemouratritaeniafrom the family Nemouridae (Insecta: Plecoptera) were sequenced. TheMesonemourametafiligeramitogenome was a 15,739 bp circular DNA molecule, which was smaller than that ofM.tritaenia(15,778 bp) due to differences in the size of the A+T-rich region. Results show that gene content, gene arrangement, base composition, and codon usage were highly conserved in two species. Ka/Ks ratios analyses of protein-coding genes revealed that the highest and lowest rates were found in ND6 and COI and that all these genes were evolving under purifying selection. All tRNA genes in nemourid mitogenomes had a typical cloverleaf secondary structure, except for tRNASer(AGN)which appeared to lack the dihydrouridine arm. The multiple alignments of nemourid lrRNA and srRNA genes showed that sequences of three species were highly conserved. All the A+T-rich region included tandem repeats regions and stem-loop structures. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results. Amphinemurinae and Nemourinae were sister-groups and the family Nemouridae was placed as sister to Capniidae and Taeniopterygidae.

scholarly journals Mitochondrial genomes of three Tetrigoidea species and phylogeny of Tetrigoidea

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4002 ◽  
Author(s):  
Li-Liang Lin ◽  
Xue-Juan Li ◽  
Hong-Li Zhang ◽  
Zhe-Min Zheng
Keyword(s):  
Rrna Genes ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Data Sets ◽  
Rich Region ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Level Identification

The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region. The order and orientation of the gene arrangement pattern were identical to that of most Tetrigoidea species. Some conserved spacer sequences between trnS(UCN) and nad1 were useful to identify Tetrigoidea and Acridoidea. The Ka/Ks value of atp8 between Trachytettix bufo and other four Tetrigoidea species indicated that some varied sites in this gene might be related with the evolution of T. bufo. The three Tetrigoidea species were compared with other Caelifera. At the superfamily level, conserved sequences were observed in intergenic spacers, which can be used for superfamily level identification between Tetrigoidea and Acridoidea. Furthermore, a phylogenomic analysis was conducted based on the concatenated data sets from mitogenome sequences of 24 species of Orthoptera in the superorders Caelifera and Ensifera. Both maximum likelihood and bayesian inference analyses strongly supported Acridoidea and Tetrigoidea as forming monophyletic groups. The relationships among six Tetrigoidea species were (((((Tetrix japonica, Alulatettix yunnanensis), Formosatettix qinlingensis), Coptotettix longjiangensis), Trachytettix bufo), Thoradonta obtusilobata).

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

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 609 ◽  
Author(s):  
Weijian Huang ◽  
Yalin Zhang
Keyword(s):  
Nucleotide Diversity ◽  
Tandem Repeats ◽  
Sliding Window ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Gene Data ◽  
Complete Mitochondrial Genomes

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)).

scholarly journals The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7633 ◽  
Author(s):  
Jun Wang ◽  
Xin-Yi Dai ◽  
Xiao-Dong Xu ◽  
Zi-Yi Zhang ◽  
Dan-Na Yu ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Gene Rearrangement ◽  
Transcription Termination ◽  
Mitochondrial Genomes ◽  
Rich Region ◽  
Conserved Motif ◽  
Intergenic Spacers ◽  
Repeat Units ◽  
Loss Models ◽  
Complete Mitochondrial Genomes

Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.

scholarly journals Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae)

ZooKeys ◽  
2020 ◽  
Vol 969 ◽  
pp. 23-42
Author(s):  
Qiu Zhongying ◽  
Chang Huihui ◽  
Yuan Hao ◽  
Huang Yuan ◽  
Lu Huimeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Mitochondrial Genomes ◽  
Rich Region ◽  
Stem Loop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Relationship Of ◽  
Complete Mitochondrial Genomes

In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.

scholarly journals Gene characteristics of the complete mitochondrial genomes of Paratoxodera polyacantha and Toxodera hauseri (Mantodea: Toxoderidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4595 ◽  
Author(s):  
Le-Ping Zhang ◽  
Yin-Yin Cai ◽  
Dan-Na Yu ◽  
Kenneth B. Storey ◽  
Jia-Yong Zhang
Keyword(s):  
Tandem Duplication ◽  
Mitochondrial Genomes ◽  
Coding Region ◽  
Rich Region ◽  
Praying Mantis ◽  
Protein Coding ◽  
Sister Clade ◽  
The Family ◽  
Intergenic Regions ◽  
Complete Mitochondrial Genomes

The family Toxoderidae (Mantodea) contains an ecologically diverse group of praying mantis species that have in common greatly elongated bodies. In this study, we sequenced and compared the complete mitochondrial genomes of two Toxoderidae species, Paratoxodera polyacantha and Toxodera hauseri, and compared their mitochondrial genome characteristics with another member of the Toxoderidae, Stenotoxodera porioni (KY689118). The lengths of the mitogenomes of T. hauseri and P. polyacantha were 15,616 bp and 15,999 bp, respectively, which is similar to that of S. porioni (15,846 bp). The size of each gene as well as the A+T-rich region and the A+T content of the whole genome were also very similar among the three species as were the protein-coding genes, the A+T content and the codon usages. The mitogenome of T. hauseri had the typical 22 tRNAs, whereas that of P. polyacantha had 26 tRNAs including an extra two copies of trnA-trnR. Intergenic regions of 67 bp and 76 bp were found in T. hauseri and P. polyacantha, respectively, between COX2 and trnK; these can be explained as residues of a tandem duplication/random loss of trnK and trnD. This non-coding region may be synapomorphic for Toxoderidae. In BI and ML analyses, the monophyly of Toxoderidae was supported and P. polyacantha was the sister clade to T. hauseri and S. porioni.

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