Mitochondrial gene rearrangement and phylogenetic relationships in the Amphilepidida and Ophiacanthida (Echinodermata, Ophiuroidea)

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

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

Genes ◽

10.3390/genes12081134 ◽

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.

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Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽

10.11646/zootaxa.4952.2.7 ◽

2021 ◽

Vol 4952 (2) ◽

pp. 331-353

Author(s):

CHAO YANG ◽

LE ZHAO ◽

QINGXIONG WANG ◽

HAO YUAN ◽

XUEJUAN LI ◽

...

Keyword(s):

Secondary Structure ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Comparative Analyses ◽

Protein Coding Genes ◽

Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies.

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The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

Insects ◽

10.3390/insects12111025 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1025

Author(s):

Sam Pedro Galilee Ayivi ◽

Yao Tong ◽

Kenneth B. Storey ◽

Dan-Na Yu ◽

Jia-Yong Zhang

Keyword(s):

Next Generation Sequencing ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Next Generation ◽

Protein Coding ◽

Protein Coding Genes ◽

Next Generation Sequencing Ngs ◽

Mt Genome ◽

Generation Sequencing

The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

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Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a025999 ◽

1998 ◽

Vol 15 (8) ◽

pp. 1009-1016 ◽

Cited By ~ 76

Author(s):

A. Arndt ◽

M. J. Smith

Keyword(s):

Sea Cucumber ◽

Gene Rearrangement ◽

Mitochondrial Gene

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A nuclear mutation that post-transcriptionally blocks accumulation of a yeast mitochondrial gene product can be suppressed by a mitochondrial gene rearrangement

Journal of Molecular Biology ◽

10.1016/0022-2836(84)90178-5 ◽

1984 ◽

Vol 175 (4) ◽

pp. 431-452 ◽

Cited By ~ 54

Author(s):

Peter P. Müller ◽

Michelle K. Reif ◽

Shen Zonghou ◽

Christian Sengstag ◽

Thomas L. Mason ◽

...

Keyword(s):

Gene Product ◽

Gene Rearrangement ◽

Mitochondrial Gene ◽

Nuclear Mutation

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Sequence amplification and gene rearrangement in parasitic nematode mitochondrial DNA.

Genetics ◽

10.1093/genetics/120.3.707 ◽

1988 ◽

Vol 120 (3) ◽

pp. 707-712

Author(s):

B C Hyman ◽

J L Beck ◽

K C Weiss

Keyword(s):

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Dna Sequences ◽

Gene Rearrangement ◽

Tandem Repeats ◽

Parasitic Nematode ◽

Mitochondrial Gene ◽

Sequence Organization ◽

Large Size ◽

Mitochondrial Gene Order

Abstract The nematode Romanomermis culicivorax, an obligate mosquito parasite, possesses a 26 kilobase (kb) mitochondrial genome. The unusually large size is due to transcriptionally active DNA sequences present as 3.0 kb direct tandem repeats and as inverted portions of the repeating unit located elsewhere in the mitochondrial DNA (mtDNA). The genome rearrangements involved in establishing this unusual sequence organization may have dramatically altered conventional mitochondrial gene order. Genes for subunits of the cytochrome c oxidase complex (COI and COII) are normally closely linked in animal mtDNAs, but are separated by approximately 8 kb in this mitochondrial genome.

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The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences

Zootaxa ◽

10.11646/zootaxa.3150.1.3 ◽

2012 ◽

Vol 3150 (1) ◽

pp. 59

Author(s):

XIAOMING GU ◽

HUI WANG ◽

RONGRONG CHEN ◽

YINGZHOU TIAN ◽

SONG LI

Keyword(s):

Mitochondrial Dna ◽

Bayesian Inference ◽

Maximum Likelihood ◽

16S Rdna ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Mitochondrial Gene ◽

Sister Group ◽

Species Group ◽

Close Phylogenetic Relationship

We examined phylogenetic relationships among newst of the genus Paramesotriton using partial mitochondrial gene se-quences, including the ND2-tRNATyr region (1415 bp) and the 12S rDNA-tRNAVal -16S rDNA region (1774 bp), from 42individuals of 10 recognized Paramesotriton species and outgroups by Bayesian inference (BI), Maximum likelihood(ML) and Maximum Parsimony (MP) methods. We found that, (1) Laotriton laoensis is the sister group of Paramesotri-ton, (2) the genus Paramesotriton is monophyletic, composed of either the P. caudopunctatus species group and the P.chinensis species group, or the subgenera Allomesotriton and Paramesotriton (3) P. longliensis and P. zhijinensis shouldbe placed in the P. caudopunctatus species group or subgenus Allomesotriton; (4) P. fuzhongensis is not a junior synonym of P. chinensis, and there is a close phylogenetic relationship between P. fuzhongensis and P. guangxiensis.

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