First pathogenomic insights into Ganoderma ellipsoideum as an emerging causal agent of basal stem rot in oil palm

Ganoderma ellipsoideum Hapuar., T.C. Wen and K.D. Hyde is a newly identified pathogenic species causing basal stem rot (BSR) in oil palm in India, yet its genetic underpinnings remain uncharacterized. We present the first first draft/contig-level genomeof G. ellipsoideum (41.6 Mb, 56.01% GC, N50 = 36,014 bp), which is 97% complete with 11,939 predicted genes and 13,434 predicted transcripts. A diverse ligninolytic enzyme arsenal (14 laccases, 24 peroxidases) was also identified. Phylogenomic analysis positions G. ellipsoideum closely with G. boninense. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases reveal many genes responsible for metabolism, signalling, and protein turnover. Glycoside hydrolases (GH) (48.7%) and glycosyltransferases (GT) (24.1%) were identified as the most abundant carbohydrate-active enzymes (CAZymes) highlighting the plant cell wall degradation capabilities of this fungus. In addition, nonribosomal peptide synthetase (NRPS)-like clusters (94%) and type I polyketide synthase (T1PKS) clusters (6%) that were related to secondary metabolite biosynthesis werewere predicted. A total of 1,662 simple sequence repeats (SSR), mainly trinucleotide repeats, and over 212 pathogenicity-associated genes including virulence homologs (FKS1, Mcs1, Chs3) were mined from the genome. This first genomic resource lays a foundation for elucidating pathogenicity, guiding breeding for resistance, and developing management strategies against BSR in oil palm.