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

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 a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽

10.1371/journal.pone.0242541 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242541

Author(s):

Lvpei Du ◽

Shanya Cai ◽

Jun Liu ◽

Ruoyu Liu ◽

Haibin Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Cold Seep ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Future Studies ◽

Protein Coding Genes ◽

High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future 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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The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

ZooKeys ◽

10.3897/zookeys.925.47820 ◽

2020 ◽

Vol 925 ◽

pp. 73-88

Author(s):

Chaoyi Hu ◽

Shuaibin Wang ◽

Bisheng Huang ◽

Hegang Liu ◽

Lei Xu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Gc Content ◽

Sister Group ◽

Rrna Genes ◽

Sister Group Relationship ◽

Trna Genes ◽

Protein Coding ◽

Generation Sequencing ◽

Simple Sequence

Scolopendra mutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S. mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S. mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S. mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S. mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.

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Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

BMC Evolutionary Biology ◽

10.1186/s12862-020-01683-8 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Dong Liu ◽

Yuanyuan Zhang ◽

Ming Zhang ◽

Jinquan Yang ◽

Wenqiao Tang

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Trees ◽

Morphological Evolution ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

12S Rrna ◽

Trna Genes ◽

Protein Coding ◽

Jaw Apparatus ◽

Intergenic Regions

Abstract Background The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. Results We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. Conclusions This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

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Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis

ZooKeys ◽

10.3897/zookeys.1005.57592 ◽

2020 ◽

Vol 1005 ◽

pp. 57-72

Author(s):

I-Chen Wang ◽

Hung-Du Lin ◽

Chih-Ming Liang ◽

Chi-Chun Huang ◽

Rong-Da Wang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Phylogenetic Trees ◽

Complete Mitochondrial Genome ◽

Genomic Variation ◽

Rrna Genes ◽

Valid Species ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes

The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.

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Complete mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

Belgian Journal of Zoology ◽

10.26496/bjz.2015.52 ◽

2020 ◽

Vol 145 (2) ◽

Author(s):

Fei Ye ◽

Ting Liu ◽

Wenbo Zhu ◽

Ping You

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Close Relationship

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata, consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania. We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra.

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New insights into Oniscidea (Crustacea: Isopoda) mitogenome structural features and phylogenetic placement of targeted taxa using mitogenomic and nuclear data

10.21203/rs.3.rs-25479/v2 ◽

2021 ◽

Author(s):

Lina Yang ◽

Ruru Chen ◽

Rui Zhang ◽

Andreas C. Dimitriou ◽

Jianmei An

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Nuclear Genome ◽

Nuclear Data ◽

Sister Group ◽

Structural Features ◽

Rrna Genes ◽

Sister Group Relationship ◽

Trna Genes ◽

Protein Coding

Abstract Among Isopoda suborders the Oniscidea has the highest species richness, and is also the largest terrestrial group in the Crustacea. Terrestrial isopods are an excellent case to study adaptations related to sea-land transition. However, the monophyly of Oniscidea and the relationships of the main lineages has been debated over the last three decades. Aiming to further explore structural features of mitochondrial genome and investigate the phylogenetic relationships within Oniscidea, the mitogenomes and a series of nuclear markers of the oniscids Ligia exotica and Mongoloniscus sinensis were sequenced. The nuclear genome was represented by four nuclear genes analyzed in a separate dataset. The mitogenomes of L. exotica and M. sinensis were 16,018 and 14,978 bp in length, respectively. Both included 13 protein-coding genes, 2 rRNA genes, and 21 and 19 tRNA genes respectively, missing one and three tRNA genes respectively compared to the isopod ground pattern. The M. sinensis mitogenome had higher average A+T content (~75.3%) than any other isopod studied to date. Phylogenetic analyses confirmed the assignment of M. sinesis to Agnaridae, as well as the sister-group relationship of the family with Porcellionidae, one of the more derived Crinochaeta clades. On the other hand, the basal position of Ligia within Oniscidea and the close evolutionary relationship with the aquatic groups Valvifera, Shaperomatida and some Cymothoidea that were included in our analysis, is indicated.

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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 of the plant bug Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae: Bryocorinae: Dicyphini)

Zootaxa ◽

10.11646/zootaxa.3554.1.2 ◽

2012 ◽

Vol 3554 (1) ◽

pp. 30 ◽

Cited By ~ 14

Author(s):

XUN DAI ◽

HUAIZHU XUN ◽

JIAN CHANG ◽

JIANGUO ZHANG ◽

BAOWEN HU ◽

...

Keyword(s):

Mitochondrial Genome ◽

Control Region ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Sister Group ◽

Nucleotide Composition ◽

Start Codon ◽

Trna Genes ◽

Nesidiocoris Tenuis

Nesidiocoris tenuis (Reuter) is a zoophytophagous mirid which is considered both as a significant natural enemy and an important pest of crops. The complete mitochondrial genome (mitogenome) of N. tenuis was determined using long PCR and a primer walking sequencing strategy. The genome is 17, 544 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (lrRNA and srRNA), and a duplicate control region. The gene order of this newly sequenced genome is identical with the ground plan of insects. The nucleotide composition is biased toward adenine and thymine with a high AT content (75.0%). The most frequent codons are ATA, TTA, TTT, and ATT. All the PCGs initiate with the standard start codon ATN. All tRNAs have the classic cloverleaf structures, with the exception of tRNASer(UCG), which lacks the dihydrouridine (DHU) arm. Secondary structures of the two ribosomal RNAs were shown referring to previous models. Variable numbers of tandem repeats were detected in the control region. The phylogenetic analyses shows that N. tenuis is the sister group to Lygus lineolaris (Palisot de Beauvois).

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The first complete mitochondrial genome of Cheyletus malaccensis (Acari: Cheyletidae): gene rearrangement

Systematic and Applied Acarology ◽

10.11158/saa.25.8.6 ◽

2020 ◽

Vol 25 (8) ◽

pp. 1433-1443

Author(s):

Yang-ming Lan ◽

Shi-qian Feng ◽

Li-yuan Xia ◽

Zhi-hong Li ◽

Yang Cao ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mite Species ◽

Rrna Genes ◽

Morphological Identification ◽

Trna Genes ◽

Protein Coding ◽

Food Commodities ◽

Cheyletus Malaccensis

The predatory mite Cheyletus malaccensis (Acari: Cheyletidae), commonly occurring in stores of various food commodities, is an important natural enemy of stored product pests. Disentangling the mt genome sequence of C. malaccensis at molecular level can decrease uncertainties during morphological identification and is useful in reconstructing the phylogeny of Acariformes group. In this study, the complete mitogenome of C. malaccensis was sequenced by the next-generation sequencing. After assembly and annotation, we found the circular 14,732 bp mitogenome of C. malaccensis, containing 13 protein coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Compared with the ancestral mitogenome organization of arthropods, most of tRNA were truncated without D-arm or/and TψC-arm. Rearrangement was found in 12 mitogenome genes. Phylogenetic analyses based on the mitogenome data from other 29 mite species were inferred by Bayesian and maximum likelihood methods, which strongly supported the closer relationship between C. malaccensis and Tetranychidae than other mites. The obtained results represent the first complete mitochondrial genome record for Cheyletidae group. It may help improve molecular phylogenetic relationship and population genetics of the Cheyletidae.

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