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

BACKGROUND: Mitochondrial (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....

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Autores principales: Xue, Xiao-Feng, Deng, Wei, Qu, Shao-Xuan, Hong, Xiao-Yue, Shao, Renfu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006854/
https://www.ncbi.nlm.nih.gov/pubmed/29914378
http://dx.doi.org/10.1186/s12864-018-4868-6
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author Xue, Xiao-Feng
Deng, Wei
Qu, Shao-Xuan
Hong, Xiao-Yue
Shao, Renfu
author_facet Xue, Xiao-Feng
Deng, Wei
Qu, Shao-Xuan
Hong, Xiao-Yue
Shao, Renfu
author_sort Xue, Xiao-Feng
collection PubMed
description BACKGROUND: Mitochondrial (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. RESULTS: We 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. CONCLUSIONS: Our 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4868-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-60068542018-06-26 The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost? Xue, Xiao-Feng Deng, Wei Qu, Shao-Xuan Hong, Xiao-Yue Shao, Renfu BMC Genomics Research Article BACKGROUND: Mitochondrial (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. RESULTS: We 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. CONCLUSIONS: Our 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4868-6) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-18 /pmc/articles/PMC6006854/ /pubmed/29914378 http://dx.doi.org/10.1186/s12864-018-4868-6 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Xue, Xiao-Feng
Deng, Wei
Qu, Shao-Xuan
Hong, Xiao-Yue
Shao, Renfu
The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?
title The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?
title_full The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?
title_fullStr The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?
title_full_unstemmed The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?
title_short The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?
title_sort mitochondrial genomes of sarcoptiform mites: are any transfer rna genes really lost?
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006854/
https://www.ncbi.nlm.nih.gov/pubmed/29914378
http://dx.doi.org/10.1186/s12864-018-4868-6
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