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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #308092
Title: Genomic prediction and validation of Pospiviroidae-derived small RNAs and their targets during tomato infection

Author
item AVINA-PADILLA, KATIA - Guanajuato Campus Of Cinvestav
item MARTINEZ DE LA VEGA, OCTAVIO - Guanajuato Campus Of Cinvestav
item RIVERA-BUSTAMENTE, RAFAEL - Guanajuato Campus Of Cinvestav
item MARTINEZ-SORIANO, JUAN PABLO - Guanajuato Campus Of Cinvestav
item OWENS, ROBERT - Retired ARS Employee
item Hammond, Rosemarie
item VIELLE-CALZADA, JEAN PHILLIPPE - Guanajuato Campus Of Cinvestav

Submitted to: Gene
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2015
Publication Date: 4/8/2015
Publication URL: http://www.journals.elsevier.com/gene/
Citation: Avina-Padilla, K., Martinez De La Vega, O., Rivera-Bustamente, R., Martinez-Soriano, J., Owens, R.A., Hammond, R., Vielle-Calzada, J. 2015. Genomic prediction and validation of Pospiviroidae-derived small RNAs and their targets during tomato infection. Gene. 564:197-205.

Interpretive Summary: Yield losses caused by viroids (small noncoding infectious RNAs) can reach 17-64% depending on the viroid strain and plant crop species. Viroid systemic infection is commonly associated with the expression of severe symptoms related to a general delay in plant physiological stages (eg., stunting, epinasty, leaf distortion, veinal chlorosis, reduction of flower size, flower abortion, reduction and alteration of fruits). To develop effective measures to combat viroid infection, it is important to understand the molecular mechanisms by which viroid RNAs cause these changes in their hosts. In this study, we used the combined approach of predictive bioinformatics to identify potential host gene targets of small viroid-related RNAs generated in plants during infection and analysis of the expression of selected target genes in the leaves and flowers of infected plants. The expression of these genes was modified during viroid infection in tomato, suggesting that bioinformatics predictions could lead to the identification of unexpected interactions between viroid RNAs and their host plant genomes. The results of our research will be of interest to scientists who are developing new approaches for the study of host/pathogen interactions and methods for pathogen control.

Technical Abstract: Viroids are small, covalently-closed, circular non-coding RNAs that act as pathogens in flowering plants. It is proposed that the symptoms of viroid pathogenesis result from a direct interaction between the viroid genomic RNA and unknown host plant factors. Using a comparative genomic approach we took advantage of the detailed annotation of the Arabidopsis thaliana (Arabidopsis) genome to identify sequence homologies between putative viroid-derived small RNAs and coding regions in the plant genome. Using this strategy we identified putative host gene targets that may be involved in symptom expression in viroid-infected tomato plants. In this communication, we report gene expression changes of two in silico-predicted tomato genes related with flower development during different viroid infection stages. We identified and analyzed 619 sequence homologies between Pospiviroidae viroid genomes and the Arabidopsis genome. The potential target sites of 20 to 21 nucleotides (nt) viroid-derived sRNAs (vd-sRNAs) were primarily distributed in the upper strand (nt. 40-75) of the P and TR domains of the viroid genome. Our predicted analysis resulted in the identification of 52 well-annotated genes that constitute potential targets of the corresponding vd-sRNAs, and two of them were selected for molecular validation. We analyzed changes in gene expression of SolBIGPETAL1 and SolOVULEABORTION6, two tomato genes that are conserved in Arabidopsis and are involved in flower development. Our results indicated that the expression of both genes was affected by the progression of Tomato planta macho viroid and Mexican papita viroid infection, a result that is in agreement with phenotypic symptoms affecting floral size. Our approach proved to be useful for the identification of two natural host genes containing sequence homologies with segments of the Pospiviroidae genome. Both are functionally conserved in Arabidopsis and tomato reproductive development, and their expression is modified during viroid infection in tomato, suggesting that the comparison of the Arabidopsis genome to reported viroid sequences could lead to the identification of unexpected interactions between viroid RNAs and their host plant genome.