Local and systemic transcriptome and spliceome changes induced by Meloidigyne incognita in tomato roots.

The aim of study is to investigate DEGs, long non-coding RNAs and alternative splicing events in the development of galls and neighboring region compared to the non-infected whole root induced by root-knot nematode (RKN, Meloidogyne incognita). Total RNA was extracted, ribosomal depleted libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovaSeq 6000. High quality, paired-end reads were then aligned to the tomato reference genome (Heinz1706 assembly SL4.0) and uniquely mapped reads were counted using Htseq. Finally, differentially expressed genes (DEGs) between whole roots-galls and whole roots-neighboring region were identified using DESeq package and downstream analyses were performed. Overall design: Susceptible Heinz1706 tomato plants were grown and 10-days-old plants were inoculated with 1000 second-stage juvenile(J2) M.incognita. 4 and 11 days post inoculation, galls, neighboring region which is two near side of galls and non-infected whole roots were collected as three biological replicates.