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