Title: NGS on nematode resistant and susceptible tomato species
Abstract:
The research work includes the transcriptome analysis of tomato genotypes viz., AT-3 (S. lycopersicum), SL 12s0 (S. lycopersicum), LA 1777 (S. habrochaites) and LA 2157 (S. arcanum) under nematode, M. incognita (nematode) stress. The sequencing was done on the Illumina MiSeq platform and yielded 5.24 GB of raw data. Overall alignment with reference sequences of Solanum lycopersicum assembly SL3.0 was found at 85.60% and with M. incognita V3 was 9.80%. AT-3 (S. lycopersicum), SL 120 (S. lycopersicum), LA 1777 (S. habrochaites), and LA 2157 (S. arcanum) aligned with tomato reference genome with a similarity of 75.37%, 82.05%, 73.04%, and 69.24% respectively. The BlastX result showed that 80.76% of blasted sequences got mapped and 73.07% were annotated. Maximum sequences (up to 94%) were mapped with UniProtKB. The top Blast hit was for S. lycopersicum followed by S. pennellii. The highest evidence code distribution was found for IEA (Inferred from Electronic Annotation). The highest enzyme code distribution was obtained for hydrolases. Gene ontology is acquired for defense response, response to stress, response to fungus, and response to biotic stimulus. PC1 captured 41.3% variance and PC2 represented 31.2%. Differential gene expression was illustrious for chitinase activity, PAL, SAM, BURP, and peroxidases. All the transcripts of nematode-infected tomato samples had 85 KEGG pathways. The validation of the defense-related genes through real-time PCR was attained for genes of chitinase, pathogenesis-related, LeHSP, SAM, LYC WRKY, and MYB TF.
