Genome-wide identification of oil palm (Elaeis guineensis Jacq.) chitinases and their response to Ganoderma boninense Pat. infection

Abstract

The basal stem rot disease caused by Ganoderma boninense Pat. is a serious problem in oil palm plantation. Naturally, plant cells produce chitinases to protect themselves from chitin-containing parasites, particularly fungi. This study employed the advance of sequencing technology and availability of oil palm genomic and transcriptomic data to identify all chitinases in oil palm genome. Homology study using the combination of BLAST and HMM methods successfully identified 35 chitinases in oil palm which comprised of 22 GH18 and 13 GH19 family members. A multiple sequence alignment method classified those chitinases into class I, II, III, IV, V, VII and an unknown class. Chitinase domains analysis against PFAM databases showed more than half of chitinases possess partial domains of GH 18 or GH 19 in their sequences. Transcriptome analysis revealed that most of GH 18 family members were expressed specifically in roots under G. boninense infection treatment. Differently, most of GH 19 members were expressed constitutively in any tissues and under biotic stress conditions. This suggests that some GH 18 members might play an important role during host defence mechanism