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

Parasites & Vectors

Xing-Quan Xia¹  Rui Feng²  Yan Wang²  Jiao-Yang Xu²  Yu Fang²  Xuan Su²  Ying Fang²  Wei-Xi Fang²  Ze-Tao Zuo²  Ling-Miao Chu²  En-Tao Sun²  Jie-Gen Yu³  Fang-Yuan Dong⁴  Xue-Bing Zhan⁴  Qian Luo⁴  Bing Chen⁴ 

[1] College of Life Science, the Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, 241000, Wuhu, Anhui Province, People’s Republic of China;Department of Health Inspection and Quarantine, Wannan Medical College, 241002, Wuhu, Anhui Province, People’s Republic of China;Department of Management Science, Wannan Medical College, 241002, Wuhu, Anhui Province, People’s Republic of China;Department of Pathology, Wannan Medical College, 241002, Wuhu, Anhui Province, People’s Republic of China;

关键词: Oribatid mites;    Mitochondrial genome;    TRNA re-annotation;    Phylogeny;   

DOI  :  10.1186/s13071-021-04719-0

来源: Springer

【 摘 要 】

BackgroundThe 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.MethodsThe 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.ResultsThe 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.ConclusionsThe 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

【 授权许可】

CC BY