Characterization of small RNAs and their targets of Fusarium oxysporum infected and non-infected cotton seedlings

Authors: SHAPULATOV, UMIDJON - Uzbekistan Academy Of Sciences; BURIEV, ZABARDAST - Uzbekistan Academy Of Sciences; Ulloa, Mauricio; Saha, Sukumar; DEVOR, ERIC - University Of Iowa; AYUBOV, MIRZAKAMOL - Uzbekistan Academy Of Sciences; NOROV, TOHIR - Uzbekistan Academy Of Sciences; SHERMATOV, SHUKHRAT - Uzbekistan Academy Of Sciences; ABDUKARIMOV, ABDUSATTOR - Uzbekistan Academy Of Sciences; Jenkins, Johnie; ABDURAKHMONOV, IBROKHIM - Uzbekistan Academy Of Sciences

Submitted to: Plant Molecular Biology Reporter
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2015
Publication Date: 6/9/2016
Citation: Shapulatov, U.M., Buriev, Z.T., Ulloa, M., Saha, S., Devor, E.J., Ayubov, M.S., Norov, T.M., Shermatov, S.E., Abdukarimov, A., Jenkins, J.N., Abdurakhmonov, I.Y. 2016. Characterization of small RNAs and their targets of Fusarium oxysporum infected and non-infected cotton seedlings. Plant Molecular Biology Reporter. 34:698-707.

Interpretive Summary: Small double-stranded ribonucleic acid (RNA) segments averaging 22 nucleotides (nt), now called small RNA (sRNAs) or micro RNAs (miRNAs) play an important role in regulating gene expression and influencing the output of many protein-coding genes. These small fragments or signatures are key components of plant basal defense response. sRNA research will continue to expand as more of their regulatory targets and functions are discovered. In recent years, miRNAs have been shown to be important in several biological processes, including plant resistance, biotic and abiotic stresses. In this study, we characterized sRNA or miRNA profiles during Fusarium oxysporum f.sp. vasinfectum (FOV) race 3 pathogenesis in cotton (Gossypium hirsutum L.) seedlings. Fusarium wilt disease, caused by FOV, is one of the most devastating diseases in cotton and many other cash crops. This disease spread from a few infected plants in a field to many production fields in all counties of California within the span of 2001-2008. A similar sequence of events was first observed in Australia in 1993 and recently in the Republic of Uzbekistan in 2009. Analysis of target proteins from sRNA signatures detected important cellular components helping us to increase our understanding of the FOV pathogenesis regulation in cotton. sRNA and miRNA sequence signatures characterized from this work will be helpful for understanding molecular mechanisms of the host defense response in cotton and for developing innovative biotechnology tools to improve FOV resistance of cotton cultivars.

Technical Abstract: In this study, we characterized small RNA (sRNA) or microRNA (miRNA) profiles during Fusarium oxysporum f.sp. vasinfectum (FOV) race 3 pathogenesis in cotton (Gossypium hirsutum L.) seedlings. sRNAs or miRNA are known to play important roles in gene expression, including stress responses, influencing the output of many protein-coding genes. From four cDNA libraries of non-infected and FOV race 3 infected roots of susceptible (' 11970) and highly tolerant (Mabane-1) genotypes 4,179 clones were sequenced, and 4,116 16 to 30 nucleotide (nt) length candidate sRNA sequences were identified. Although the total number of sequences was approximately similar among libraries, these tag-sequences were substantially different based on length distribution. The highest number of tagged signatures were those 21 nt in length in all of the libraries. Further, more than 73 percentof sRNAs matched Gossypium (G. arboretum L., G. hirsutum, and G. barbadense L.) ESTs. A small percentage of sRNAs matched A.thaliana (1.68percent), T. cacao (1.26 percent), fungal (2 percent), and other organism (21.33 percent ) ESTs. Homology analyses in MirBase database showed 4 percent of sRNAs to be homologous to previously reported plant miRNAs. From these analyses, we identified only two miRNAs not registered in the cotton database: Mir-160 (highly conserved in plants), which was sequenced from FOV uninfected Mabane-1 young root tissues, and Mir-2911, which was sequenced from all four sRNA libraries and has been reported in Nicotiana tabacum L. and Populus euthratica L. databases. Analysis of target proteins from sRNA signatures detected important cellular components helping us to increase our understanding of the FOV pathogenesis regulation in cotton. sRNA and miRNA sequence signatures characterized from this work will be helpful for understanding molecular mechanisms of the host defense response in cotton and for developing innovative biotechnology tools to improve FOV resistance of cotton cultivars.