Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications

To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).

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

Insects ◽

10.3390/insects12040338 ◽

2021 ◽

Vol 12 (4) ◽

pp. 338

Author(s):

Yan Jiang ◽

Hao-Xi Li ◽

Xiao-Fei Yu ◽

Mao-Fa Yang

Keyword(s):

Stop Codon ◽

Phylogenetic Analyses ◽

Initiation Site ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Phylogenetic Implications ◽

Rna Genes ◽

Complete Mitochondrial Genomes

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.

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Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae)

Insects ◽

10.3390/insects11040232 ◽

2020 ◽

Vol 11 (4) ◽

pp. 232

Author(s):

Nan Zhou ◽

Yanling Dong ◽

Pingping Qiao ◽

Zhaofu Yang

Keyword(s):

Control Region ◽

Ostrinia Nubilalis ◽

Phylogenetic Analyses ◽

Structural Elements ◽

Ostrinia Furnacalis ◽

Protein Coding ◽

Phylogenetic Implications ◽

Ostrinia Scapulalis ◽

The Relationship ◽

Rna Genes

To understand mitogenome characteristics and reveal phylogenetic relationships of the genus Ostrinia, including several notorious pests of great importance for crops, we sequenced the complete mitogenomes of four species: Ostrinia furnacalis (Guenée, 1854), Ostrinia nubilalis (Hübner, 1796), Ostrinia scapulalis (Walker, 1859) and Ostrinia zealis (Guenée, 1854). Results indicate that the four mitogenomes—O. furnacalis, O. nubilalis, O. scapulalis, and O. zealis—are 15,245, 15,248, 15,311, and 15,208 bp in size, respectively. All four mitogenomes are comprised of 37 encoded genes and a control region. All 13 protein-coding genes (PCGs) initiate with ATN and terminate with TAN, with the exception of cox1 that starts with CGA, and cox1, cox2, and nad5 that terminate with an incomplete codon T. All transfer RNA genes (tRNAs) present the typical clover-leaf secondary structure except for the trnS1 (AGN) gene. There are some conserved structural elements in the control region. Our analyses indicate that nad6 and atp6 exhibit higher evolution rates compared to other PCGs. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods revealed the relationship (O. palustralis + (O. penitalis + (O. zealis + (O. furnacalis + (O. nubilalis + O. scapulalis))))) within Ostrinia.

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Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications

Insects ◽

10.3390/insects12121049 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1049

Author(s):

Huifeng Zhao ◽

Ye Chen ◽

Zitong Wang ◽

Haifeng Chen ◽

Yaoguang Qin

Keyword(s):

Stop Codon ◽

Phylogenetic Analyses ◽

Strong Support ◽

Sister Group ◽

Nucleotide Composition ◽

Start Codon ◽

Protein Coding ◽

Phylogenetic Implications ◽

Molecular Phylogenetic ◽

Rna Genes

The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.

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Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽

10.3390/genes12081185 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1185

Author(s):

Wenqian Wang ◽

Huan Zhang ◽

Jérôme Constant ◽

Charles R. Bartlett ◽

Daozheng Qin

Keyword(s):

Control Region ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Start Codon ◽

Rrna Genes ◽

Rich Region ◽

Protein Coding ◽

Phylogenetic Implications ◽

Rna Genes ◽

Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

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Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽

10.3390/insects12080754 ◽

2021 ◽

Vol 12 (8) ◽

pp. 754

Author(s):

Yupeng Wu ◽

Hui Fang ◽

Jiping Wen ◽

Juping Wang ◽

Tianwen Cao ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Trna Genes ◽

Cox1 Gene ◽

Protein Coding ◽

Phylogenetic Implications ◽

Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

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

Insects ◽

10.3390/insects11080534 ◽

2020 ◽

Vol 11 (8) ◽

pp. 534 ◽

Cited By ~ 1

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.

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

PeerJ ◽

10.7717/peerj.12465 ◽

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.

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Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

Journal of Medical Entomology ◽

10.1093/jme/tjab152 ◽

2021 ◽

Author(s):

Shu-Tong Dai ◽

Dian-Xing Feng ◽

Da-Peng Sun

Keyword(s):

Mitochondrial Genome ◽

Species Identification ◽

Stop Codon ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genomes ◽

Base Pairs ◽

Protein Coding ◽

Phylogenetic Studies ◽

Rna Genes ◽

Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

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Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

Amphibia-Reptilia ◽

10.1163/156853810791769464 ◽

2010 ◽

Vol 31 (3) ◽

pp. 299-309 ◽

Cited By ~ 8

Author(s):

Peng Yan ◽

Ge Feng ◽

Xiaoqiang Li ◽

Xiaobing Wu

Keyword(s):

Phylogenetic Analyses ◽

Sister Group ◽

Molecular Data ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Nucleotide Level ◽

Protein Coding ◽

Genome Features ◽

Gavialis Gangeticus ◽

Complete Mitochondrial Genomes

AbstractThe complete mitochondrial (mt) genomes of two crocodilians: Crocodylus palustris and Crocodylus mindorensis, were sequenced in order to examine their gene and genome features. Additionally, we intended to increase the amount of molecular data suitable for phylogenetic analysis. Their gene orders conform to other crocodilians that have been sequenced, except the arrangement of two tRNA genes differ from other vertebrates, showing that the gene order of crocodilians is remarkably conserved. Phylogenetic analyses (maximum likelihood, Bayesian inference) based on the mt protein-coding genes at the nucleotide level were performed among crocodilians for which complete mt genomes were available. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, that constitutes a sister group to traditional Crocodylidae. In this report, Mecistops cataphractus is evidently most closely related to Osteolaemus tetraspis. They are isolated as sister taxon from the main clades in Crocodylus. Regarding Paleosuchus, it appears as sister group to Caiman within the Alligatoridae. In particular, relationships among species of Crocodylus (true crocodiles) are discussed.

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Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽

10.3390/genes10080563 ◽

2019 ◽

Vol 10 (8) ◽

pp. 563 ◽

Cited By ~ 2

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.

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