(P39) Identification of lncRNAs transcriptionally active during tomato immune response

POMBO M; LAUFF D; ROSLI H

Quilmes, Buenos Aires

Encuentro; II Argentine Meeting on Biology of Non-coding RNAs; 2018

UNQ

Plants have evolved a two-layered immune response against pathogens. Pattern-triggeredimmunity (PTI) is activated as consequence of the perception of microbe-associated molecularpatterns (MAMPs) through pattern recognition receptors (PRRs) and leads to cell wallreinforcement, reactive oxygen species (ROS) production, etc. Some pathogenic bacteria such asPseudomonas syringae pv. tomato (Pst) are able to deliver using a type 3 secretion system,effector proteins into the plant cell cytoplasm. Effectors manipulate cell metabolism favoringbacterial proliferation. Resistant plants are able to detect the activity of effectors by means ofresistance (R) proteins, leading to the activation of effector-triggered immunity (ETI) usuallyassociated to a hypersensitive response (HR) that allows controlling bacterial population growth.Both PTI and ETI activation result in large transcriptomic changes that have been studied in thepast years using RNA-seq. In this work we reanalyzed previously generated data from tomatoleaves challenged with MAMPs and Pst mutants in order to identify novel transcripts that areputative long non-coding RNAs (lncRNAs). Filtering these novel transcripts (22,595) by length>200 bp, open reading frame length <300 bp, low coding potential and no homology to Pfam andRfam databases, 2048 transcripts were considered as putative lncRNAs. These belonged todifferent categories based on their relation to annotated transcripts: j, at least one junction match(873); i, fully contained in reference intron (274); o, same strand overlap with reference exon (155);u, unknown intergenic (943); x, exonic overlap with opposite strand (364). Overall lncRNA sizedistribution ranged between 200 and 6615 bp (median 413 bp). Transcript abundance had amedian of 4 FPKM, nearly 10 fold less than that of tomato annotated coding transcripts (45 FPKM).Analysis of lncRNA intron-exon structure, revealed that for those belonging to j and o categoriesprevailed 2-exon type, while single-exon type was more abundant for i, u and x. Differentialtranscript abundance analysis allowed the identification of lncRNAs induced and suppressed(corrected p <0.05) during early (30 min) and late (6h) PTI induction and ETI (6 h) induction. Wehave selected a small set of these, based on their transcript induction rate to study theirparticipation in tomato immunity using virus induced gene silencing (VIGS).