Draft genome sequence of fastidious pathogen Ceratobasidium theobromae , which causes vascular-streak dieback in Theobroma cacao

, a member of the family, is the causal agent of vascular-streak dieback (VSD) of cacao, a major threat to the chocolate industry in the South-East Asia. The fastidious pathogen is very hard to isolate and maintain in pure culture, which is a major bottleneck in the study of its genetic diversity and genome. This study describes for the first time, a 33.90 Mbp de novo assembled genome of a putative isolate from cacao. Ab initio gene prediction identified 9264 protein-coding genes, of which 800 are unique to when compared to spp., a closely related group. Transcriptome analysis using RNA isolated from 4 independent VSD symptomatic cacao stems identified 3550 transcriptionally active genes when compared to the assembled genome while transcripts for only 4 genes were detected in 2 asymptomatic stems. De novo assembly of the non-cacao associated reads from the VSD symptomatic stems uniformly produced genes with high identity to predicted genes in the genome as compared to spp. or genes found in Genbank. Further analysis of the predicted transcriptome was carried out identifying CAZy gene classes, KEGG-pathway associated genes, and 138 putative effector proteins. These findings put forth, for the first time, a predicted genome for the fastidious basidiomycete causing VSD on cacao providing a model for testing and comparison in the future. The genome predicts a pathogenesis model involving secreted effector proteins to suppress plant defense mechanisms and plant cell wall degrading enzymes.