Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

Mitochondrial genome evolution in pelagophyte algae

Genome Biology and Evolution ◽

10.1093/gbe/evab018 ◽

2021 ◽

Author(s):

Shannon J Sibbald ◽

Maggie Lawton ◽

John M Archibald

Keyword(s):

Mitochondrial Genome ◽

Harmful Algal Blooms ◽

Algal Blooms ◽

23S Rrna ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Unique Region ◽

Long Read ◽

Genomic Studies ◽

Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

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Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽

10.1186/s12864-021-07859-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wen-Ge Dong ◽

Yalun Dong ◽

Xian-Guo Guo ◽

Renfu Shao

Keyword(s):

Mitochondrial Genome ◽

Control Region ◽

Genome Organization ◽

Trna Gene ◽

Trna Genes ◽

Single Chromosome ◽

Gene Translocation ◽

Sucking Lice ◽

Different Types ◽

Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

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Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

Scientific Reports ◽

10.1038/s41598-021-81622-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kun Zhang ◽

Kehua Zhu ◽

Yifan Liu ◽

Hua Zhang ◽

Li Gong ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Rearrangement ◽

Tandem Duplication ◽

Mitochondrial Gene ◽

Gene Arrangement ◽

Protein Coding ◽

Muraenesox Cinereus ◽

Complete Mitogenome ◽

Relationship Of ◽

Rna Genes

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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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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The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

Journal of Helminthology ◽

10.1017/s0022149x18000871 ◽

2018 ◽

Vol 94 ◽

Cited By ~ 3

Author(s):

P. Zhang ◽

R.K. Ran ◽

A.Y. Abdullahi ◽

X.L. Shi ◽

Y. Huang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Squirrel Monkey ◽

Complete Mitochondrial Genome ◽

Mitochondrial Gene ◽

Rrna Genes ◽

Saimiri Sciureus ◽

Trna Genes ◽

Loop Structure ◽

Protein Coding ◽

Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

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The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae

Zootaxa ◽

10.11646/zootaxa.4363.4.3 ◽

2017 ◽

Vol 4363 (4) ◽

pp. 506

Author(s):

HUAXUAN LIU ◽

LIYUN YAN ◽

GUOFANG JIANG

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Taxonomic Status ◽

Polymerase Chain Reaction Method ◽

Ribosomal Rna Genes ◽

Start Codon ◽

Trna Genes ◽

Rna Genes

In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively. All 13 mitochondrial PCGs shared the start codon ATN. Twelve of the PCGs ended with termination codon TAA and TAG, while cytochrome coxidase subunit 1 (COI) utilized an incomplete T as terminator codon. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes were 1379 bp and 794 bp, respectively. The A+T rich region was 798 bp in length and contained 88.5% AT content. A phylogenetic analysis based on 13 PCGs by using Bayesian inference (BI) and maximum likelihood (ML) revealed that Sinopodisma is not monophyletic group. We think that the name and taxonomic status of S. tsinlingensis are right, and it should not be moved into the genus Pedopodisma. These data will provide important information for a better understanding of the population genetics and species identification for Sinopodisma.

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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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Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)

10.1101/228882 ◽

2017 ◽

Author(s):

Gisele Lopes Nunes ◽

Renato Renison Moreira Oliveira ◽

Eder Soares Pires ◽

Santelmo Vasconcelos ◽

Thadeu Pietrobon ◽

...

Keyword(s):

Mitochondrial Genome ◽

Base Composition ◽

Iron Ore ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Significant Advance ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Rich Region ◽

The Public

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.

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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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The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

Systematic and Applied Acarology ◽

10.11158/saa.27.1.9 ◽

2022 ◽

Author(s):

Tianhong Wang ◽

Zihao Wang ◽

Ruwei Bai ◽

Zhijun Yu ◽

Jingze Liu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Trna Genes ◽

Illumina Hiseq ◽

Protein Coding ◽

Haemaphysalis Qinghaiensis ◽

Mitogenome Sequence ◽

Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

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