scholarly journals The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9932 ◽  
Author(s):  
Hong-Ling Liu ◽  
Qing-Dong Chen ◽  
Song Chen ◽  
De-Qiang Pu ◽  
Zhi-Teng Chen ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Scale Insects ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Planococcus Citri ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Stem Loop

The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).

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 Novel mitochondrial genes and gene reannotation: conservation of gene arrangements among available astigmatid mites

2020 ◽  
Author(s):  
Yu Fang ◽  
Jiaoyang Xu ◽  
Xuebing Zhan ◽  
Weixi Fang ◽  
Fangyuan Dong ◽  
...  
Keyword(s):  
Rrna Genes ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Stem Loop ◽  
Protein Coding ◽  
Coding Regions ◽  
Internal Structures ◽  
Complete Mitogenome ◽  
Astigmatid Mites

Abstract Background Mitochondrial genomes (mitogenomes) of metazoans typically contain 37 genes, comprising 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. To date, complete mitogenome sequences of 15 species of Astigmatina are available, and they present variation in a number of features, such as gene arrangements, tRNA unconventional secondary structures, and the number and internal structures of control regions. Furthermore, 11 astigmatid mites from six superfamilies share the same gene arrangement. Two available species from the genus Histiostoma reportedly have different mitochondrial (mt) tRNA gene arrangements. Results We sequenced the mitogenomes of Lepidoglyphus destructor and Gohieria fusca, both from the superfamily Glycyphagoidea (Astigmatina). In total, 37 mt genes were identified in the two Glycyphagoidea species. Based on AT content and stem-loop structures, we divided the largest non-coding regions (LNRs) in L. destructor and G. fusca into two domains, respectively. The novel feature of two domains for the LNR was also found in Acalvolia sp. (Astigmatina, Hemisarcoptoidea). Using MITOS 2, tRNAScan, ARWEN, and manual approaches, we reannotated the mitogenomes of Histiostoma blomquisti, H. feroniarum, and Trouessartia rubecula. We reannotated six tRNA genes in H. blomquisti and four tRNA genes in H. feroniarum. We were able to identify all of the mt tRNA genes that were reported as lost in Tr. rubecula. The phylogenetic relationships found in our study were fairly consistent with previous studies of astigmatid mites phylogeny. Within Astigmatina, Glycyphagoidea was recovered as a monophyletic group. Conclusions A novel feature of the LNR was found in L. destructor, G. fusca and Acalvolia sp. (Astigmatina, Hemisarcoptoidea). This feature was not found in other available Astigmatina mitochondrial sequences. In the current study, most available astigmatid mitochondrial genomes shared the same consistent gene arrangement that could be the potential ancestral pattern in Astigmatina.

scholarly journals Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

scholarly journals Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

2019 ◽  
Vol 20 (20) ◽  
pp. 5167 ◽  
Author(s):  
Qiang Li ◽  
Yuanhang Ren ◽  
Xiaodong Shi ◽  
Lianxin Peng ◽  
Jianglin Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Time ◽  
Dynamic Changes ◽  
Protein Coding ◽  
Tree Topologies ◽  
Nuclear Genomes

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

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).

A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

2014 ◽  
Vol 35 (3) ◽  
pp. 331-343 ◽  
Author(s):  
Yongmin Li ◽  
Huabin Zhang ◽  
Xiaoyou Wu ◽  
Hui Xue ◽  
Peng Yan ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar)

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 739-747 ◽  
Author(s):  
T. HUYSE ◽  
L. PLAISANCE ◽  
B. L. WEBSTER ◽  
T. A. MO ◽  
T. A. BAKKE ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Ribosomal Rna ◽  
Trna Gene ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mt Genome

SUMMARYIn the present study, we describe the complete mitochondrial (mt) genome of the Atlantic salmon parasite Gyrodactylus salaris, the first for any monogenean species. The circular genome is 14 790 bp in size. All of the 35 genes recognized from other flatworm mitochondrial genomes were identified, and they are transcribed from the same strand. The protein-coding and ribosomal RNA (rRNA) genes share the same gene arrangement as those published previously for neodermatan mt genomes (representing cestodes and digeneans only), and the genome has an overall A+T content of 65%. Three transfer RNA (tRNA) genes overlap with other genes, whereas the secondary structure of 3 tRNA genes lack the DHU arm and 1 tRNA gene lacks the TΨC arm. Eighteen regions of non-coding DNA ranging from 4 to 112 bp in length, totalling 278 bp, were identified as well as 2 large non-coding regions (799 bp and 768 bp) that were almost identical to each other. The completion of the mt genome offers the opportunity of defining new molecular markers for studying evolutionary relationships within and among gyrodactylid species.

scholarly journals Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera: Sphingidae)

ZooKeys ◽  
2018 ◽  
Vol 754 ◽  
pp. 127-139 ◽  
Author(s):  
Jun Li ◽  
Rui-Rui Lin ◽  
Yao-Yao Zhang ◽  
Kun-Jie Hu ◽  
Ya-Qi Zhao ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Oxidase Subunit ◽  
Relationship Of

In the present study, the complete mitogenome of Theretrajaponica was sequenced and compared with other sequenced mitogenomes of Sphingidae species. The mitogenome of T.japonica, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) and a region rich in adenine and thymine (AT-rich region), is a circular molecule with 15,399 base pairs (bp) in length. The order and orientation of the genes in the mitogenome are similar to those of other sequenced mitogenomes of Sphingidae species. All 13 protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome C oxidase subunit 1 gene (cox1) which is initiated by the codon CGA as observed in other lepidopteran insects. Cytochrome C oxidase subunit 2 gene (cox2) has the incomplete termination codon T and NADH dehydrogenase subunit 1 gene (nad1) terminates with TAG while the remainder terminates with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Ile and Leu2 are the most frequently used codon families and codons CGG, CGC, CCG, CAG, and AGG are absent. The 431 bp AT-rich region includes the motif ATAGA followed by a 23 bp poly-T stretch, short tandem repeats (STRs) of TC and TA, two copies of a 28 bp repeat ‘ATTAAATTAATAAATTAA TATATTAATA’ and a poly-A element. Phylogenetic analyses within Sphingidae confirmed that T.japonica belongs to the Macroglossinae and showed that the phylogenetic relationship of T.japonica is closer to Ampelophagarubiginosa than Daphnisnerii. Phylogenetic analyses within Theretra demonstrate that T.japonica, T.jugurtha, T.suffusa, and T.capensis are clustered into one clade.

scholarly journals Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Meng-Yuan Zhao ◽  
Qing-Bo Huo ◽  
Yu-Zhou Du
Keyword(s):  
Ribosomal Rna ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Stem Loop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Noncoding Control Region ◽  
Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

scholarly journals The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaolin Li ◽  
Lijiao Li ◽  
Zhijie Bao ◽  
Wenying Tu ◽  
Xiaohui He ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Fungal Species ◽  
Ectomycorrhizal Fungus ◽  
Open Reading Frames ◽  
Rrna Genes ◽  
Trna Genes ◽  
Total Size ◽  
Protein Coding

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

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