Complete mitochondrial genomes of four species of praying mantises (Dictyoptera, Mantidae) with ribosomal second structure, evolutionary and phylogenetic analyses

Praying mantises are distributed all over the world. Though some Mantodea mitogenomes have been reported, an evolutionary genomic and phylogenetic analysis study lacks the latest taxonomic system. In the present study, four new mitogenomes were sequenced and annotated. Deroplatys truncate, D. lobate, Amorphoscelis chinensis and Macromantis sp. belong to Deroplatyidae, Amorphoscelidae and Photinaidae family, respectively. Our results indicated that the ATP8 gene may be lost in D. truncate and D. lobata mt genome, and four tRNA genes have not been found in D. truncate, D. lobata and Macromantis sp. A dN/dS pair analysis was conducted and it was found that all genes have evolved under purifying selection. Furthermore, we tested the phylogenetic relationships between the eight families of the Mantodea, including 35 species of praying Mantis. Based on the complete mitochondrial genome data, it was also suggested as sister to Deroplatyidae + Mantidae, Metallyticus sp., the only representative of Metallyticidae, is sister to the remaining mantises. Our results support the taxonomic system of Schwarz and Roy and are consistent with previous studies.

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Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

Bioscience Reports ◽

10.1042/bsr20182349 ◽

2019 ◽

Vol 39 (8) ◽

Author(s):

Jian-Qiu Li ◽

Li Li ◽

Bao-Quan Fu ◽

Hong-Bin Yan ◽

Wan-Zhong Jia

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Evolutionary Relationship ◽

Sister Group ◽

Trna Genes ◽

Mammal Species ◽

Qinghai Province ◽

Loop Region ◽

Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

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Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽

10.3897/zookeys.1070.72742 ◽

2021 ◽

Vol 1070 ◽

pp. 13-30

Author(s):

Wanqing Zhao ◽

Dajun Liu ◽

Qian Jia ◽

Xin Wu ◽

Hufang Zhang

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Purifying Selection ◽

Sister Group ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

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The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea

Zootaxa ◽

10.11646/zootaxa.4243.1.5 ◽

2017 ◽

Vol 4243 (1) ◽

pp. 125 ◽

Cited By ~ 21

Author(s):

YING WANG ◽

JINJUN CAO ◽

WEIHAI LI

Keyword(s):

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Simple Loop ◽

Interspecific Divergence ◽

Family Level ◽

Mt Genome

We present the complete mitochondrial (mt) genome sequence of the stonefly, Styloperla spinicercia Wu, 1935 (Plecoptera: Styloperlidae), the type species of the genus Styloperla and the first complete mt genome for the family Styloperlidae. The genome is circular, 16,129 base pairs long, has an A+T content of 70.7%, and contains 37 genes including the large and small ribosomal RNA (rRNA) subunits, 13 protein coding genes (PCGs), 22 tRNA genes and a large non-coding region (CR). All of the PCGs use the standard initiation codon ATN except ND1 and ND5, which start with TTG and GTG. Twelve of the PCGs stop with conventional terminal codons TAA and TAG, except ND5 which shows an incomplete terminator signal T. All tRNAs have the classic clover-leaf structures with the dihydrouridine (DHU) arm of tRNASer(AGN) forming a simple loop. Secondary structures of the two ribosomal RNAs are presented with reference to previous models. The structural elements and the variable numbers of tandem repeats are described within the control region. Phylogenetic analyses using both Bayesian (BI) and Maximum Likelihood (ML) methods support the previous hypotheses regarding family level relationships within the Pteronarcyoidea. The genetic distance calculated based on 13 PCGs and two rRNAs between Styloperla sp. and S. spinicercia is provided and interspecific divergence is discussed.

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Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

Genes ◽

10.3390/genes10090724 ◽

2019 ◽

Vol 10 (9) ◽

pp. 724 ◽

Cited By ~ 1

Author(s):

Xiaolei Yu ◽

Wei Tan ◽

Huanyu Zhang ◽

Weiling Jiang ◽

Han Gao ◽

...

Keyword(s):

Mitochondrial Genome ◽

Control Region ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Ground Beetle ◽

Purifying Selection ◽

Trna Genes ◽

Stem Loop ◽

Protein Coding

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.

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The Complete Mitochondrial Genome ofCtenoptilum vasava(Lepidoptera: Hesperiidae: Pyrginae) and Its Phylogenetic Implication

Comparative and Functional Genomics ◽

10.1155/2012/328049 ◽

2012 ◽

Vol 2012 ◽

pp. 1-13 ◽

Cited By ~ 48

Author(s):

Jiasheng Hao ◽

Qianqian Sun ◽

Huabin Zhao ◽

Xiaoyan Sun ◽

Yonghua Gai ◽

...

Keyword(s):

Stop Codon ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Rich Region ◽

Extra Copy ◽

Protein Coding ◽

Natural Group ◽

Protein Coding Genes ◽

Mt Genome

We here report the first complete mitochondrial (mt) genome of a skipper,Ctenoptilum vasavaMoore, 1865 (Lepidoptera: Hesperiidae: Pyrginae). The mt genome of the skipper is a circular molecule of 15,468 bp, containing 2 ribosomal RNA genes, 24 putative transfer RNA (tRNA), genes including an extra copy of trnS (AGN) and a tRNA-like insertion trnL (UUR), 13 protein-coding genes and an AT-rich region. All protein-coding genes (PCGs) are initiated by ATN codons and terminated by the typical stop codon TAA or TAG, except for COII which ends with a single T. The intergenic spacer sequence between trnS (AGN) and ND1 genes also contains the ATACTAA motif. The AT-rich region of 429 bp is comprised of nonrepetitive sequences, including the motif ATAGA followed by an 19 bp poly-T stretch, a microsatellite-like (AT)3(TA)9element next to the ATTTA motif, an 11 bp poly-A adjacent to tRNAs. Phylogenetic analyses (ML and BI methods) showed that Papilionoidea is not a natural group, and Hesperioidea is placed within the Papilionoidea as a sister to ((Pieridae+Lycaenidae)+Nymphalidae) while Papilionoidae is paraphyletic to Hesperioidea. This result is remarkably different from the traditional view where Papilionoidea and Hesperioidea are considered as two distinct superfamilies.

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Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae

Journal of Helminthology ◽

10.1017/s0022149x19000932 ◽

2019 ◽

Vol 94 ◽

Cited By ~ 1

Author(s):

Y. Li ◽

X.X. Ma ◽

Q.B. Lv ◽

Y. Hu ◽

H.Y. Qiu ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Coding Region ◽

Closely Related Species ◽

Protein Coding ◽

The Family ◽

Mt Genome ◽

High Statistical Support

Abstract Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1–3, nad 1–6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.

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The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

Scientific Reports ◽

10.1038/s41598-021-93946-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ying-ying Ye ◽

Jing Miao ◽

Ya-hong Guo ◽

Li Gong ◽

Li-hua Jiang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Bootstrap Support ◽

Trna Genes ◽

Gene Rearrangements ◽

Phylogenetic Studies ◽

Gc Skew ◽

Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

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Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China

PeerJ ◽

10.7717/peerj.7853 ◽

2019 ◽

Vol 7 ◽

pp. e7853 ◽

Cited By ~ 1

Author(s):

Yuchen Yan ◽

Gengyun Niu ◽

Yaoyao Zhang ◽

Qianying Ren ◽

Shiyu Du ◽

...

Keyword(s):

Mitochondrial Genome ◽

New Genus ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Sister Group ◽

Morphological Characters ◽

Trna Genes ◽

Sequencing Data ◽

Link Type

Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.

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Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

International Journal of Molecular Sciences ◽

10.3390/ijms21113778 ◽

2020 ◽

Vol 21 (11) ◽

pp. 3778

Author(s):

Changwei Bi ◽

Na Lu ◽

Yiqing Xu ◽

Chunpeng He ◽

Zuhong Lu

Keyword(s):

Phaseolus Vulgaris ◽

Mitochondrial Genome ◽

Common Bean ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Comparative Genomic ◽

Trna Genes ◽

Leguminous Plants ◽

The Common

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

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Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca

10.21203/rs.3.rs-112827/v1 ◽

2020 ◽

Author(s):

Yan Cheng ◽

Xiaoxue He ◽

S. V. G. N. Priyadarshani ◽

Yu Wang ◽

Li Ye ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Sandy Beaches ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Landscape Plant ◽

Suaeda Glauca ◽

Mt Genome ◽

Mitochondria Genome

Abstract Background Suaeda glauca is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also a beautiful landscape plant with high development prospects and scientific research value. The S. glauca chloroplast genome has recently been reported; however, the mitochondria genome is still unexplored. Results This study assembled the mitochondria genome and annotated the mitochondrial genes of S. glauca based on the Pacbio long reads. The circular mitochondrial genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (27.96%), T (28.01%), C (21.64%), G (21.64%). S. glauca mt genome has 51 genes, including 26 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Phylogenetic analysis with common genes of 28 species resulted in similar morphological classification. Conclusions As a Chenopodiaceae species, S. glauca mt genome will provide insights into the missing pieces in the evolution of sex determination and improve genomic breeding in the future.

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