The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?

Shao-Xuan Qu,Renfu Shao,Wei Deng,Xiao-Yue Hong,Xiao-Feng Xue

doi:10.1186/s12864-018-4868-6

Abstract

BackgroundMitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus; loss of 2–3 tRNA genes was reported in Tyrophagus longior, T. putrescentiae and Sarcoptes scabiei. Nevertheless, convincing evidence for mt gene loss is lacking in these mites.ResultsWe sequenced the mitochondrial genomes of two sarcoptiform mites, Histiostoma feroniarum (13,896 bp) and Rhizoglyphus robini (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of H. feroniarum and R. robini, respectively. The other six mt tRNA genes in H. feroniarum and five mt tRNA genes in R. robini can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in St. magnus, two of the three mt tRNA genes that were reported as lost in T. longior and T. putrescentiae, and the two mt tRNA genes that were reported as lost in Sa. scabiei. All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems.ConclusionsOur results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.

Highlights

Mitochondrial genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA genes and 22 transfer RNA genes
Using tRNAscan-SE [26] and ARWEN [27] programs, we identified 16 and 17 transfer RNA (tRNA) genes in the mt genomes of H. feroniarum and R. robini
The other six mt tRNA genes of H. feroniarum and the other five mt tRNA genes of R. robini could only be identified manually by sequence alignment and secondary structure comparison with those identified in other species of sarcoptiform mites [8, 15, 18, 20,21,22,23,24,25, 28]

Summary

Introduction

Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. The entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Convincing evidence for mt gene loss is lacking in these mites. Mt genomes typically have 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes [2]. Mites and ticks (subclass Acari) represent a major group (> 54,000 species) in the class Arachnida [10] and colonize a wide range of terrestrial, marine and aquatic habitats [11]. The order Sarcoptiformes comprises approximately 16,300 extant species [12].

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