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

Authors: ALI, SHAHIN - University Of California, Davis; ASMAN, ASMAN - Hassanudin University; Shao, Jonathan; FIRMANSYAH, AMANDA - Muhammadiyah University Of Makassar; SUSILO, AGUNG - Indonesian Coffee And Cocoa Research Institute; ROSAMANA, ADE - Hassanudin University; MCMAHON, PETER - University Of Sydney; JUNAID, MUHAMMAD - Hassanudin University; GUEST, DAVID - University Of Sydney; KHENG, TEE YEI KHENG - Malaysian Cocoa Board; Meinhardt, Lyndel; Bailey, Bryan

Submitted to: Fungal Biology and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2019
Publication Date: 9/30/2019
Citation: Ali, S., Asman, A., Shao, J.Y., Firmansyah, A., Susilo, A., Rosamana, A., Mcmahon, P., Junaid, M., Guest, D., Kheng, T., Meinhardt, L.W., Bailey, B.A. 2019. Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback (VSD) in Theobroma cacao. Fungal Biology and Biotechnology. 6:14.

Interpretive Summary: Significant amounts of the world’s supply of cacao, the source of chocolate, are produced by the island nations of Southeast Asia. The disease vascular streak dieback is found only in Southeast Asia and has caused significant losses in yield. The symptoms of vascular streak dieback include death of branches and, in some cases, death of whole trees. To make thing worse, the fungal pathogen causing vascular streak dieback, Ceratobasidium theobromae, is very difficult to grow in pure culture. Thus, obtaining information on the genetic makeup of the pathogen has proven difficult to impossible, until now. Our objective was to obtain DNA from the VSD pathogen and sequence its genome. A very small amount of the fungus was grown in pure culture and limited amounts of DNA were extracted from the fungus. That DNA was sequenced and the genome of Ceratobasidium theobromae was assembled for the first time. In addition, all the genes possessed by the fungus were identified in the genome sequence. This sequence provides researchers with a vast reservoir of potential markers for studying the genetic diversity of the pathogen. Only by understanding the pathogen’s genetic diversity, can breeders have confidence in developing cacao varieties with long-lasting resistance to the pathogen causing vascular streak dieback of cacao.

Technical Abstract: Ceratobasidium theobromae, a member of the Ceratobasidiaceae 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 obtain 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 33.92 Mb de novo assembled genome of a putative C. theobromae isolate from cacao. Ab initio gene prediction identified 9,270 protein-coding genes, of which 800 are unique to C. theobromae when compared to Rhizoctonia solani, another closely related Ceratobasidiaceae species. Transcriptome analysis using RNA isolated from 4 independent cacao stems showing symptoms of VSD identified 3,551 transcriptionally active genes when compared to the assembled C. theobromae genome while transcripts for only 4 C. theobromae 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 C. theobromae genome as compared to Rhizoctonia solani or genes found in Genbank. Further analysis of the predicted C. theobromae 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 C. theobromae causing VSD on cacao and providing a model for testing and comparison in the future. The C. theobromae genome predicts a pathogenesis model involving secreted effector proteins to suppress plant defense mechanism and plant cell wall degrading enzymes.