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

Insects ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 869
Author(s):  
Jiu Tang ◽  
Weijian Huang ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Relationships ◽  
Nucleotide Diversity ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Structural Features ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
First Time

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))).

scholarly journals Five Mitochondrial Genomes of the GenusEysarcoris Hahn, 1834 with Phylogenetic Implications for the Pentatominae (Hemiptera: Pentatomidae)

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 597
Author(s):  
Rongrong Li ◽  
Min Li ◽  
Jiang Yan ◽  
Ming Bai ◽  
Hufang Zhang
Keyword(s):  
Phylogenetic Relationships ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Repeat Units ◽  
Phylogenetic Implications ◽  
The Relationship

Four complete mitogenomes of Eysarcoris rosaceus, E. montivagus, E. gibbosus, E. annamita and one near-complete mitochondrial genome of E. ventralis were sequenced and used to explore the phylogenetic relationships of tribes within the subfamily Pentatominae. The mitogenomes range from 15,422 to 16,043 base pairs (bp) in length and encode 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes (21 in E. ventralis), and a control region. Similar to other heteropteran species, the AT contents of the sequenced species were higher than their GC contents. The most frequently used start/stop codon was ATN/TAA. GTG was only found in atp6 and atp8 of E. gibbosus. All transfer RNA genes (tRNAs) exhibit the typical cloverleaf secondary structure, except for the trnS1 and trnV, which lacks the stem of the DHU arm. The length and copy number of repeat units were conserved within Eysarcoris, with the exception of E. gibbosus. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods strongly supported the relationship among tribes within Pentatominae and confirmed that Graphosoma should be an intermediate lineage of Pentatominae. The relationship between Eysarcoris and Carbula was strongly supported and combined with our previous geometric morphometrics and chromosomal studies, suggest the Eysarcoris should belong to the tribe Eyasrcorini. This work will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in Pentatominae.

scholarly journals The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 533
Author(s):  
Lei Cui ◽  
Rongbo Cao ◽  
Yuelei Dong ◽  
Xingchen Gao ◽  
Jingyi Cen ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Complete Mitogenome ◽  
First Time ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species.

scholarly journals Characterization of the Complete Mitochondrial Genome of Drabescus ineffectus and Roxasellana stellata (Hemiptera: Cicadellidae: Deltocephalinae: Drabescini) and Their Phylogenetic Implications

Insects ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 534 ◽  
Author(s):  
Deliang Xu ◽  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Strong Support ◽  
Start Codon ◽  
Protein Coding ◽  
Simple Loop ◽  
Repeat Units ◽  
Phylogenetic Implications

To explore the mitogenome characteristics and shed light on the phylogenetic relationships and molecular evolution of Drabescini species, we sequenced and analyzed the complete mitochondrial genome of two species including Drabescus ineffectus and Roxasellana stellata. The complete mitogenomes of D. ineffectus and R. stellata are circular, closed and double-stranded molecules with a total length of 15744 bp and 15361 bp, respectively. These two newly sequenced mitogenomes contain the typical 37 genes. Most protein-coding genes (PCGs) began with the start codon ATN and terminated with the terminal codon TAA or TAG, with an exception of a special initiation codon of ND5, which started with TTG, and an incomplete stop codon T-- was found in the Cytb, COX2, ND1 and ND4. All tRNAs could be folded into the canonical cloverleaf secondary structure except for the trnS1, which lacks the DHU arm and is replaced by a simple loop. The multiple tandem repeat units were found in A + T-control region. The sliding window, Ka/Ks and genetic distance analyses indicated that the ATP8 presents a high variability and fast evolutionary rate compared to other PCGs. Phylogenetic analyses based on three different datasets (PCG123, PCG12R and AA) using both Bayesian inference (BI) and maximum likelihood (ML) methods showed strong support for the monophyly of Drabescini.

scholarly journals Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12465
Author(s):  
Nian Gong ◽  
Lin Yang ◽  
Xiangsheng Chen
Keyword(s):  
Nucleotide Diversity ◽  
Stop Codon ◽  
Purifying Selection ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Basal Position ◽  
High Support ◽  
Complete Mitochondrial Genomes

Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.

scholarly journals Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 563 ◽  
Author(s):  
Hu Li
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Paraphyletic Group ◽  
Complete Mitochondrial Genomes

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

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 Structural and phylogenetic implications of the complete mitochondrial genome of Ledra auditura

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jia-Jia Wang ◽  
De-Fang Li ◽  
Hu Li ◽  
Mao-Fa Yang ◽  
Ren-Huai Dai
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Coding Region ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Outgroup Species ◽  
Region Length ◽  
Branch Support

Abstract We sequenced and annotated the first complete mitochondrial genome (mitogenome) of Ledra auditura (Hemiptera: Cicadellidae: Ledrinae) and reconstructed phylogenetic relationships among 47 species (including 2 outgroup species) on the basis of 3 datasets using maximum likelihood (ML) and Bayesian inference (BI) analyses. The complete L. auditura mitogenome (length, 16,094 bp) comprises 37 genes [13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs], 1 control region, and 2 long non-coding regions. The first long non-coding region (length, 211 bp) is located between tRNA-I and tRNA-Q and the second region (length, 994 bp) between tRNA-S2 and ND1. All PCGs show ATN (Met/Ile) as their start codon and TAR as their stop codon. Except tRNA-S1 (AGN), which lacks the dihydrouridine arm, all tRNAs can fold into the typical cloverleaf secondary structure. The complete L. auditura mitogenome shows a base composition bias of 76.3% A + T (A = 29.9%, T = 46.4%, G = 13.3%, and C = 10.5%), negative AT skew of −0.22, and positive GC skew of 0.12. In ML and BI analyses, L. auditura was clustered with Evacanthus heimianus (Hemiptera: Cicadellidae: Evacanthinae) with strong branch support.

scholarly journals First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 87
Author(s):  
Lilan Yuan ◽  
Xueying Ge ◽  
Guanglin Xie ◽  
Haoyu Liu ◽  
Yuxia Yang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Repeat Sequence ◽  
Start Codon ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Independent Families ◽  
First Time

To explore the characteristics of the mitogenome of Melyridae and reveal phylogenetic relationships, the mitogenome of Cordylepherus sp. was sequenced and annotated. This is the first time a complete mitochondrial genome has been generated in this family. Consistent with previous observations of Cleroidea species, the mitogenome of Cordylepherus sp. is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. All protein-coding genes (PCGs) initiate with the standard start codon ATN, except ND1, which starts with TTG, and terminate with the complete stop codons of TAA and TAG, or incomplete forms, TA- and T-. Most tRNAs have the typical clover-leaf structure, except trnS1 (Ser, AGN), whose dihydrouridine (DHU) arm is reduced. In the A+T-rich region, three types of tandem repeat sequence units are found, including a 115 bp sequence tandemly repeated twice, a 16 bp sequence tandemly repeated three times with a partial third repeat and a 10 bp sequence tandemly repeated seven times. Phylogenetic analyses based on 13 protein-coding genes by both Bayesian inference (BI) and maximum likelihood (ML) methods suggest that Melyridae sensu lato is polyphyletic, and Dasytinae and Malchiinae are supported as independent families.

scholarly journals Structural Features and Phylogenetic Implications of Four New Mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha)

2021 ◽  
Vol 22 (3) ◽  
pp. 1348
Author(s):  
Nian Gong ◽  
Lin Yang ◽  
Xiang-Sheng Chen
Keyword(s):  
Sequence Data ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
Structural Features ◽  
Region Gene ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Phylogenetic Implications

To explore the differences in mitogenome variation and phylogenetics among lineages of the Hemiptera superfamily Fulgoroidea, we sequenced four new mitogenomes of Caliscelidae: two species of the genus Bambusicaliscelis (Caliscelinae: Caliscelini), namely Bambusicaliscelis flavus and B. fanjingensis, and two species of the genus Youtuus (Ommatidiotinae: Augilini), namely Youtuus strigatus and Y. erythrus. The four mitogenomes were 15,922–16,640 bp (base pair) in length, with 37 mitochondrial genes and an AT-rich region. Gene content and arrangement were similar to those of most other sequenced hexapod mitogenomes. All protein-coding genes (PCGs) started with a canonical ATN or GTG and ended with TAA or an incomplete stop codon single T. Except for two transfer RNAs (tRNAs; trnS1 and trnV) lacking a dihydrouridine arm in the four species and trnC lacking a dihydrouridine stem in the Youtuus species, the remaining tRNAs could fold into canonical cloverleaf secondary structures. Phylogenetic analyses based on sequence data of 13 PCGs in the 28 Fulgoroidea species and two outgroups revealed that Delphacidae was monophyletic with strong support. Our data suggest that Fulgoridae is more ancient than Achilidae. Furthermore, Flatidae, Issidae, and Ricaniidae always cluster to form a sister group to Caliscelidae.

scholarly journals Characterization of the Complete Mitochondrial Genome of Epicauta impressicornis (Coleoptera: Meloidae) and Its Phylogenetic Implications for the Infraorder Cucujiformia

2020 ◽  
Vol 20 (2) ◽  
Author(s):  
Yang-Yang Liu ◽  
Zhi-Cheng Zhou ◽  
Xiang-Sheng Chen
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Repeat Unit ◽  
Amino Acid Sequences ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Sister Relationships

Abstract The complete mitochondrial genome (mitogenome) of Epicauta impressicornis Pic (Coleoptera: Meloidae) was determined. The circular genome is 15,713-bp long, and encodes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The 13 PCGs start with the typical ATN codon and terminate with the typical stop codon TAA (ND2, ND4L, ND6, ATP6, ATP8, and CYTB), TAG (ND1 and ND3), and T- (COX1, COX2, COX3, ND4, and ND5). The two rRNA genes (rrn12S and rrn16S) are encoded on the minority strand. All tRNAs genes except trnS1 (AGN) are predicted to fold into the typical cloverleaf structure. The longest overlap (10 bp) is observed between ATP8 and ATP6. CR mainly harbors a conserved poly-T stretch (15 bp), a short repeat unit (17 bp), some universal microsatellite-like repeats, and a canonical poly-A tail. Phylogenetic analysis using Bayesian inferences and maximum likelihood based on nucleotide and corresponding amino acid sequences of the 13 PCGs showed that E. impressicornis is closely related to E. chinensis, this relationship is and supported within Cucujiformia belonging to Meloidae (Tenebrionoidea). Our results further confirmed the monophyly of Tenebrionoidea, Lymexyloidea, Curculionoidea, Chrysomeloidea, Cucujoidea, Coccinelloidea, and Cleroidea within Cucujiformia, and revealed the sister relationships of (Cleroidea + Coccinelloidea), (Lymexyloidea + Tenebrionoidea), and ((Chrysomeloidea + Cucujoidea) + Curculionoidea). We believe that the complete mitogenome of E. impressicornis will contribute to further studies on molecular bases for the classification and phylogeny of Meloidae or even Cucujiformia.

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