De novo sequence of the mitochondrial genome of Tyrophagus putrescentiae (Acari: Sarcoptiformes) including 22 tRNA sequences and the largest non-coding region

Fang, Weixi; Dong, Fangyuan; Sun, Entao; Tao, Dongdong; Wang, Yan; Xu, Jiaoyang; Yu, Fang; Zhan, Xuebing; Ye, Changjiang

doi:10.1007/s10493-020-00477-3

Cited by 5 publications

(4 citation statements)

References 29 publications

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“…1B). These conserved sequences were reported in the LNRs for Acaroidea species (Aleuroglyphus ovatus, Caloglyphus berlesei, Rhizoglyphus robini, and Tyrophagusputrescentiae), Pyroglyphidae species (Dermatophagoides pteronyssinus and D. farinae), Hemisarcoptoidea species (Acalvolia sp., Carpoglyphus lactis), and Sarcoptoidea (Psoroptes cuniculi) [22,[24][25][26]. In addition, we also found these conserved sequences in Pterolichoidea (Ardeacarus ardeae).…”

Section: Mitochondrial Genomes Of Lepidoglyphus Destructor and Gohiersupporting

confidence: 62%

“…The gene arrangement of Ty. putrescentiae was consistent with the possible common ancestor of astigmatid mites [22]. Murillo et al used COI to analyze molecular phylogenetics and suspected that a misidenti cation existed in the Ty.…”

Section: Discussionmentioning

confidence: 99%

“…Fang et al de novo sequenced and analyzed the mitochondrial genome of Ty. Putrescentiae, and identi ed the three tRNA genes that were reported as lost in a previous study [22]. In Analgoidea, ve tRNA genes (trnA, trnE, trnI, trnY, and trnV) were reported absent from Trouessartia rubecula [23].…”

Section: Introductionmentioning

confidence: 88%

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

Fang¹,

Xu²,

Zhan³

et al. 2020

Preprint

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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.

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Section: Mitochondrial Genomes Of Lepidoglyphus Destructor and Gohiersupporting

confidence: 62%

Section: Discussionmentioning

confidence: 99%

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

Fang¹,

Xu²,

Zhan³

et al. 2020

Preprint

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“…Fang et al also did not support tRNA loss. After de novo sequencing and analysis of the circular mt genome of Tyrophagus putrescentiae, they retrieved three tRNA (trnF, trnS1, trnQ) genes that previous studies were "lost" [28]. We identi ed all of the "lost" tRNAs in oribatid mites.…”

Section: Discussionmentioning

confidence: 99%

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

Zhan

Chen

Fang

et al. 2020

Preprint

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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.

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Complete mitochondrial genomes of Thyreophagus entomophagus and Acarus siro (Sarcoptiformes: Astigmatina) provide insight into mitogenome features, evolution, and phylogeny among Acaroidea mites

Sun

Fang

et al. 2022

Exp Appl Acarol

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De novo sequence of the mitochondrial genome of Tyrophagus putrescentiae (Acari: Sarcoptiformes) including 22 tRNA sequences and the largest non-coding region

Cited by 5 publications

References 29 publications

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

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

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

Complete mitochondrial genomes of Thyreophagus entomophagus and Acarus siro (Sarcoptiformes: Astigmatina) provide insight into mitogenome features, evolution, and phylogeny among Acaroidea mites

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