RNA-seq Analysis of the Molecular Interaction between Pseudomonas syringae pv. actinidiae (Psa) and the Kiwifruit

摘要

To elucidate early molecular kiwifruit plant interaction during the infection of Pseudomonas syringae pv. actinidiue (Psa), the gene expression was studied by RNA-seq at 3, 24 and 48 h after inoculation, both on acibenzolar-S-methyl (ASM)-pretreated and untreated plants. Transcriptomic analysis of Actinidia chinensis, performed using 75 bp paired end Illumina tecnology, leads to the de novo assembly of 39,607 contigs (Trinity software) with an average size of 933 bp and N50 of 1,472 bp. The annotation was done using Blast2GO: BLASTx and BLASTn were performed against the NR protein, RefSeq protein and SwissProt/UniProt databases and against NR nucleotide database, respectively (E-value cut-off le-5). The BLASTx matches were used for further GO mappings to give a putative functional annotation. The functionality InterProScan in Blast2GO software allowed to retrieve domain/motif information in the InterPro and in other domain databases. Furthermore local BLASTx alignments were made against COGs database. Reads were mapped to the contigs using the CLC software to identify differentially expressed genes (DEGs), by R package DESeq. The analyses of DEGs suggest that in ASM untreated plants the early response involves a typical defense mechanism against bacterium, but with not adequate level to counteract the infection. On the other hand, in the ASM-pretreated plants molecular mechanisms which involve also a SAR response are activated and lead the plants toward the resistance. Moreover, the RNA-seq technology has permitted to identify differentially expressed genes involved in basal defense mechanisms, but also revealed novel differentially expressed genes and transcripts of unknown functions.