Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum

BMC Genomics

Research Article

Tengfei Xiao¹  Runsheng Chen¹  Xingye Xu²  Qi Jin²  Jie Dong²  Jian Yang²  Tao Liu²  Xianwen Ren²  Lilian Sun² 

[1] Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China;MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, Beijing, China;

关键词: Trichophyton Rubrum;    snoRNA Gene;    Small Nuclear RNAs;    Potential Target Site;    ncRNA Candidate;   

DOI  :  10.1186/1471-2164-14-931

 received in 2013-09-08, accepted in 2013-12-20,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundAccumulating evidence demonstrates that non-coding RNAs (ncRNAs) are indispensable components of many organisms and play important roles in cellular events, regulation, and development.ResultsHere, we analysed the small non-coding RNA (ncRNA) transcriptome of Trichophyton rubrum by constructing and sequencing a cDNA library from conidia and mycelia. We identified 352 ncRNAs and their corresponding genomic loci. These ncRNA candidates included 198 entirely novel ncRNAs and 154 known ncRNAs classified as snRNAs, snoRNAs and other known ncRNAs. Further bioinformatic analysis detected 96 snoRNAs, including 56 snoRNAs that had been annotated in other organisms and 40 novel snoRNAs. All snoRNAs belonged to two major classes—C/D box snoRNAs and H/ACA snoRNAs—and their potential target sites in rRNAs and snRNAs were predicted. To analyse the evolutionary conservation of the ncRNAs in T. rubrum, we aligned all 352 ncRNAs to the genomes of six dermatophytes and to the NCBI non-redundant nucleotide database (NT). The results showed that most of the identified snRNAs were conserved in dermatophytes. Of the 352 ncRNAs, 102 also had genomic loci in other dermatophytes, and 27 were dermatophyte-specific.ConclusionsOur systematic analysis may provide important clues to the function and evolution of ncRNAs in T. rubrum. These results also provide important information to complement the current annotation of the T. rubrum genome, which primarily comprises protein-coding genes.

【 授权许可】

Unknown   
© Liu et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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.