scholarly journals Mitochondrial Analysis of Oribatid Mites Provides Insights into Their Atypical tRNAs Annotation, Genome Rearrangement and Evolution

2020 ◽  
Author(s):  
Xuebing Zhan ◽  
Bing Chen ◽  
Yu Fang ◽  
Fangyuan Dong ◽  
Weixi Fang ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
Trna Gene ◽  
Gene Annotation ◽  
Oribatid Mite ◽  
Systematic Position ◽  
Oribatid Mites ◽  
Single Type ◽  
Trna Genes ◽  
Manual Annotation ◽  
Mt Genome

Abstract Background: Mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Loss of genes is rare in Sarcoptiformes mite mt genomes, but two of the six previously reported oribatid mites (Acariform Order Sarcoptiformes) are reported to have lost part of their tRNA genes. To determine whether these tRNA genes were indeed lost and whether the loss of tRNAs is universal, we re-annotated all of the available oribatid mites and sequenced the mt genome of Oribatula sakamorii. Methods: The mitogenome of O. sakamorii was sequenced with Illumina Hiseq sequencer. The mt tRNA gene annotated using multi-software combined with manual annotation approach. Phylogenetic analyses of maximum likelihood (ML) and Bayesian inference (BI) were performed with both concatenated nucleotide and amino acid sequences.Results: Mt genomes of O. sakamorii contain 37 genes including 22 tRNA genes. We were able to identify all of the mt tRNA genes that were reported as lost in Steganacarus magnus and Paraleius leontonychus, and revealed some atypical tRNAs annotation errors in oribatid mites. Oribatid mite mt genomes are characterized by low rates of gene rearrangement, with six or seven gene blocks conserved between all of the oribatid mite species and the mt genome of ancestral arthropod. Considering only the relative order of the major genes (PCGs, rRNAs), only one gene or two genes were rearranged relative to the ancestral genome. Both CREx analysis and phylogenetic results supported the origin of the Astigmata within the Oribatida. We also explored the phylogenetic relationships among all of the available oribatid mites and the results also confirm the systematic position of Hermannia in the Crotonioidea superfamily. This is also supported by synapomorphic gene derived boundary.Conclusions: The tRNA "lost" phenomenon is not universal in oribatid mites. Instead of loss, we found that the highly atypical secondary structure of inferred mt tRNA genes makes them unidentifiable by a single type of tRNA search program. Multi-software combined with manual annotation approach can improve the accuracy of tRNA gene annotation. Besides, we determined the correct systematic position of Hermannia and supported the origin of astigmatid mites was from oribatid mites.

scholarly journals Mitochondrial analysis of oribatid mites provides insights into their atypical tRNA annotation, genome rearrangement and evolution

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xue-Bing Zhan ◽  
Bing Chen ◽  
Yu Fang ◽  
Fang-Yuan Dong ◽  
Wei-Xi Fang ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
Trna Gene ◽  
Gene Annotation ◽  
Oribatid Mite ◽  
Systematic Position ◽  
Amino Acid Sequences ◽  
Oribatid Mites ◽  
Single Type ◽  
Trna Genes ◽  
Manual Annotation

Abstract Background The mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Although the loss of genes is rare in Sarcoptiformes mite mitogenomes, two of the six previously reported oribatid mites (Acariforms: Sarcoptiformes) are reported to have lost parts of their tRNA genes. To confirm whether the tRNA genes were indeed lost and whether the loss is universal, we re-annotated the available oribatid mite sequences and sequenced the mitogenome of Oribatula sakamorii. Methods The mitogenome of O. sakamorii was sequenced using an Illumina HiSeq sequencer. The mt tRNA gene was annotated using multi-software combined with a manual annotation approach. Phylogenetic analyses were performed using the maximum likelihood and Bayesian inference methods with concatenated nucleotide and amino acid sequences. Results The mitogenomes of O. sakamorii contained 37 genes, including 22 tRNA genes. We identified all mt tRNA genes that were reported as “lost” in Steganacarus magnus and Paraleius leontonychus and revealed certain atypical tRNA annotation errors in oribatid mite sequences. Oribatid mite mitogenomes are characterized by low rates of genetic rearrangement, with six or seven gene blocks conserved between the mitogenome of all species and that of ancestral arthropods. Considering the relative order of the major genes (protein-coding genes and rRNAs), only one or two genes were rearranged with respect to their positions in the ancestral genome. We explored the phylogenetic relationships among the available oribatid mites, and the results confirmed the systematic position of Hermannia in the Crotonioidea superfamily. This was also supported by the synapomorphic gene-derived boundaries. Conclusions The tRNA “lost” phenomenon is not universal in oribatid mites. Rather, highly atypical secondary structure of the inferred mt tRNA genes made them unidentifiable using a single type of tRNA search program. The use of multi-software combined with a manual annotation approach can improve the accuracy of tRNA gene annotation. In addition, we identified the precise systematic position of Hermannia and validated that Astigmata is nested in Oribatida. Graphic Abstract

scholarly journals 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 ◽  
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.

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.

Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida)

2019 ◽  
Vol 187 (3) ◽  
pp. 585-598 ◽  
Author(s):  
Wei-Ning Li ◽  
Xiao-Feng Xue
Keyword(s):  
Oribatid Mite ◽  
Gene Clusters ◽  
Oribatid Mites ◽  
Phylogenetic Information ◽  
Genome Reorganization ◽  
Genome Group ◽  
High Level ◽  
The Relationship ◽  
Mt Genome ◽  
Astigmatid Mites

Abstract Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.

Mitochondrial Genome of Brugia malayi Microfilariae Isolated From a Clinical Sample

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiong Qing ◽  
Kasem Kulkeaw ◽  
Sirichit Wongkamchai ◽  
Stephen Kwok-Wing Tsui
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Gene Annotation ◽  
Clinical Sample ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Human Patient ◽  
Close Relationship ◽  
Mt Genome

Lymphatic filariasis is a neglected parasitic disease that is a leading cause of long-term disability. Information obtained from genome sequencing of filarial worm can help us identify systems in the worm that are likely to be useful for novel drug design. Brugia (B.) malayi is still the only lymphatic-dwelling filarial parasite with a nearly complete, fully annotated, and published genome. However, most previous studies were based on the FR3 strain of B. malayi, which originally was isolated from a human patient, and was adapted to the rodent model, then maintained in laboratories for more than 60 years. It is uncertain whether genetic variation exists, thus, sequencing of clinical isolates of lymphatic dwelling filarial parasites is a high priority. Here, we report for the first time the complete mitochondrial genome of B. malayi microfilariae from clinical isolate. Complete mitochondrial (mt) genome of the microfilariae isolated from a blood sample taken from a Thai subject living in Narathiwat Province, which is an endemic area of brugian filariasis, was assembled with sequencing reads obtained by Illumina sequencing. Gene annotation, phylogenetic analysis and single nucleotide polymorphism (SNP) were deployed. A complete 13,658-bp mt genome of B. malayi microfilaria was obtained, and it shows 68x coverage. Based on gene annotation, the mt genome consists of 12 protein-coding, two rRNA, and 23 tRNA genes. Phylogenetic analysis using all protein sequences of DNA sequences of mt genome or cytochrome c oxidase subunit I (COX1) revealed a close relationship among three lymphatic filariae (i.e., B. timori, zoonotic B. pahangi, and Wuchereria spp.). The SNPs in the COX1 gene can differentiate microfilariae of B. malayi in human from those found in canine. Furthermore, the number, order and transcription, and direction of B. malayi microfilariae mitochondrial genes were the same as those found in the FR3 strain of B. malayi. The comparison on mitochondrial genome of B. malayi could have important implications on the development of a new intervention or vaccine to treat or prevent this disease in endemic areas/regions around the world.

scholarly journals Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo.

1986 ◽  
Vol 6 (7) ◽  
pp. 2663-2673 ◽  
Author(s):  
M C Strobel ◽  
J Abelson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Trna Gene ◽  
Nuclear Extract ◽  
Nonsense Suppression ◽  
Trna Genes ◽  
Suppressor Activity ◽  
Specific Sequence ◽  
Made In

The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.

scholarly journals Transfer RNA genes experience exceptionally elevated mutation rates

2018 ◽  
Vol 115 (36) ◽  
pp. 8996-9001 ◽  
Author(s):  
Bryan P. Thornlow ◽  
Josh Hough ◽  
Jacquelyn M. Roger ◽  
Henry Gong ◽  
Todd M. Lowe ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Trna Gene ◽  
Gene Evolution ◽  
Purifying Selection ◽  
Mutation Rates ◽  
Model Organisms ◽  
Biological Synthesis ◽  
Human Populations ◽  
Trna Genes ◽  
Simple Method

Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations.

Oribatid mites (Acari, Oribatida) from Tam Dao National Park (Northern Vietnam), with description of two new species

2018 ◽  
Vol 23 (2) ◽  
pp. 314 ◽  
Author(s):  
Sergey G. Ermilov ◽  
Josef Stary
Keyword(s):  
New Species ◽  
Body Size ◽  
National Park ◽  
Oribatid Mite ◽  
Oribatid Mites ◽  
Oriental Region ◽  
Northern Vietnam ◽  
Two New Species ◽  
Tam Dao National Park ◽  
First Time

The present study is based on oribatid mite material (Acari, Oribatida) collected from Tam Dao National Park (Northern Vietnam) in 1988. A list of identified taxa, including 119 species from 80 genera and 47 families, is presented; of these, 13 species (Epilohmannoides rabori, Camisia spinifer, Sadocepheus undulatus, Eremobelba flexuosa, Hammerella excisa, Suctobelbella inenodabilis, Dolicheremaeus auritus, Eupelops acromios, Protoribates genitalis, Allogalumna machadoi, Carinogalumna philippinensis, Pergalumna magnipora capillaris, Galumnella nipponica) and five genera (Epilohmannoides, Camisia, Sadocepheus, Brassiella, Carinogalumna) are recorded in the Vietnamese fauna for the first time, and two species (Tokunocepheus mizusawai, Flagellozetes (Cosmogalumna) ornatus), one genus (Tokunocepheus) and one family (Tokunocepheidae) are recorded in the Oriental region for the first time. Two new species are described: Ramusella paraarcuata sp. nov. differs from Ramusella arcuata Mahunka & Mahunka-Papp, 2012 by the larger body size, lamellar setae similar in length and thickness to interlamellar setae, the presence of two or three branches on bothridial setae, and the absence of notogastral setae c. Neoribates paragracilis sp. nov. differs from Neoribates gracilis Travé, 1972 by the larger body size, and the presence of long apex (not shorter than head) on bothridial setae.

New and interesting oribatid mites (Acari, Oribatida) from Hanoi (Northern Vietnam)

2018 ◽  
Vol 23 (1) ◽  
pp. 61 ◽  
Author(s):  
Sergey G. Ermilov ◽  
Josef Stary
Keyword(s):  
New Species ◽  
Body Surface ◽  
Oribatid Mite ◽  
Oribatid Mites ◽  
Oriental Region ◽  
Northern Vietnam ◽  
Two New Species ◽  
First Time ◽  
The City

The present study is based on oribatid mite material (Acari, Oribatida) collected from the city of Hanoi in Northern Vietnam. A list of identified taxa, including 68 species from 49 genera and 32 families, is presented; of these, ten species (Trhypochthonius japonicus, Nothrus oblongus, Hermanniella aliverdievae, Arthrodamaeus decemsetiger, Arcoppia fenestralis orientalis, Ramusella puertomonttensis, Allosuctobelba grandis, Scheloribates elegans, Neoribates gracilis, Pergalumna corniculata) and one genus (Trhypochthonius) are recorded in the Vietnamese fauna for the first time; seven species (Xenillus selgae, Arcoppia curtipila, Cycloppia granulata, Hammerella gracilis, Allosuctobelba tricuspidata, Ceratozetoides maximus, Protoribates hakonensis) and one genus (Ceratozetoides) are recorded in the Oriental region for the first time. Two new species belonging to the genera Allosuctobelba and Oribatella are described: Allosuctobelba alexanderkhaustovi sp. nov. differs from Allosuctobelba tricuspidata tricuspidata Aoki, 1984 in the rostrum having three to four lateral teeth and very long notogastral setae positioned in two parallel rows; Oribatella pavelklimovi sp. nov. differs from Oribatella kunsti Bernini, 1972 by the granulate body surface, setiform  aggenital setae and the dorsolateral position of notogastral setae lm and lp.

A transcriptionally active tRNA gene interferes with nucleosome positioning in vivo

1992 ◽  
Vol 12 (9) ◽  
pp. 4015-4025
Author(s):  
R H Morse ◽  
S Y Roth ◽  
R T Simpson
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Trna Gene ◽  
Rna Polymerase Iii ◽  
Nucleosome Positioning ◽  
Yeast Cells ◽  
Trna Genes ◽  
Start Site ◽  
Cis Acting

Incorporation into a positioned nucleosome of a cis-acting element essential for replication in Saccharomyces cerevisiae disrupts the function of the element in vivo [R. T. Simpson, Nature (London) 343:387-389, 1990]. Furthermore, nucleosome positioning has been implicated in repression of transcription by RNA polymerase II in yeast cells. We have now asked whether the function of cis-acting elements essential for transcription of a gene transcribed by RNA polymerase III can be similarly affected. A tRNA gene was fused to either of two nucleosome positioning signals such that the predicted nucleosome would incorporate near its center the tRNA start site and essential A-box element. These constructs were then introduced into yeast cells on stably maintained, multicopy plasmids. Competent tRNA genes were transcribed in vivo and were not incorporated into positioned nucleosomes. Mutated, inactive tRNA genes were incorporated into nucleosomes whose positions were as predicted. This finding demonstrates that the transcriptional competence of the tRNA gene determined its ability to override a nucleosome positioning signal in vivo and establishes that a hierarchy exists between cis-acting elements and nucleosome positioning signals.

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