LOCAL AND SYSTEMIC REGULATION OF GENE EXPRESSION, ALTERNATIVE SPLICING, AND LONG NON-CODING RNAS DURING TOMATO INTERACTION WITH THE ROOT-KNOT NEMATODE MELOIDOGYNE INCOGNITA

Root-knot nematodes (Meloidogyne spp.) are obligatory root parasites that infect thousands of vascular plant species, causing significant economic losses. These highly polyphagous nematodes engage in sophisticated interactions with host plants and induce the formation of knot-like structures known as galls whose ontogeny remains largely unknown. Among all Meloidogyne species, M. incognita is considered the most damaging species, particularly in tropical and subtropical regions. The main objective of this dissertation is to understand the molecular mechanisms controlling tomato responses to M. incognita infection with the goal of identifying new genetic targets for improving tomato resistance to this destructive parasite. This was accomplished by investigating local and systemic transcriptome and splicesome reprogramming in the M. incognita-induced galls and neighboring root cells, and by identifying and functionally characterizing differentially expressed long non-coding RNAs (lncRNAs). The analysis revealed that M. incognita induces robust gene expression changes, both locally in galls and systemically in neighboring root cells, providing new insights into the coordinated cell-to-cell communications during infection. The transcriptome analysis also indicated that M. incognita exerts a firm control over the cell cycle process in order to increase nuclear ploidy levels required for feeding site formation. Spliceome analysis demonstrated that M. incognita significantly reprograms pre-mRNA splicing patterns as a total of 9064 differentially spliced events from 2898 genes were identified. Overexpression of certain splicing variants negatively impacted gall formation and/or egg mass production, supporting the functional importance of splicing mechanism during the interaction. Additionally, the abundance of a substantial number of lncRNAs were altered specifically at the early stage of infection with the large majority of these lncRNAs being downregulated. The differentially expressed lncRNAs were predicted to encode peptides that contain functional domains and mimic binding sites for microRNAs. The microRNA mimic function of lncRNAs was confirmed using transgenic hairy roots and agroinfiltration, supporting the functional roles of lncRNAs in post-transcriptional gene regulation. Together, the data documented in the current study provide foundation for future studies to functionally characterize tomato genes and lncRNAs involved in cell-to-cell communications, vesicle trafficking, cell cycle, transcriptional and post-transcriptional regulation with the ultimate goal of increasing plant resistance to parasitic nematodes.