Distinct patterns of plant gene expression are elicited by different inbred lines of the root-knot nematode, Meloidogyne hapla

Isogenic tomato plants (Solanum lycopersicum, Heinz 1706) were infected with one of two inbred M. hapla parasitic root knot nematode lines: LM and VW9. Infected root tissue samples (galls) were harvested three weeks post-infection, and RNA was extracted for RNA-Seq. This RNA contained a mixture of tomato and M. hapla transcripts. Sequencing reads were aligned to a concatenated reference of the M. hapla and tomato genomes, enabling us to measure transcript abundance for both the plant and the parasite. Tomato and M. hapla genes were then tested for differential expression between plants infected with LM nematodes and plants infected with VW9 nematodes.