Genome and transcriptome analysis of the latent pathogen lasiodiplodia Theobromae, an emerging threat to cacao industry

Authors: ALI, SHAHIN - University Of California, Davis; Shao, Jonathan; ADI, ASMAN - Hassanudin University; BALIDION, JOHNNY - University Of The Philippines; STREM, MARY - Former ARS Employee; Puig, Alina; Meinhardt, Lyndel; Bailey, Bryan

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2019
Publication Date: 10/3/2019
Citation: Ali, S., Shao, J.Y., Adi, A., Balidion, J., Strem, M., Puig, A.S., Meinhardt, L.W., Bailey, B.A. 2019. Genome and transcriptome analysis of the latent pathogen lasiodiplodia Theobromae, an emerging threat to cacao industry. Genes, Genomes, and Genomics. 63:37–52.

Interpretive Summary: Lasiodiplodia theobromae is becoming a significant threat to crops, including cacao, in many parts of the world. It causes stem cankers and diebacks in mature and young cacao trees. To understand this disease at the molecular level we sequenced the genome of this fungus and looked at fungal gene expression during the disease cycle. More than 13,000 genes were predicted, of which around 2,800 are unique to Lasiodiplodia theobromae when compared to other closely related fungi. The gene expression data show that the fungus expresses genes responsible for disrupting the plant’s defense mechanisms and degrade the plant cell-wall supporting disease development. These findings expand our knowledge on L. theobromae genes involve in disease development in cacao, and will be used by researchers and plant breeders to improve disease management practices and develop improved cacao varieties. Ultimately, the consumer could benefit through a more stable supply of high quality cacao.

Technical Abstract: Lasiodiplodia theobromae (Ltheo), a member of the Botryosphaeriaceae family, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. It causes stem cankers and diebacks in mature and young cacao trees. Under biotic stress, Ltheo can also act as a secondary or synergistic pathogen and worsened the disease scenario. While attempting to recover Ceratobasidium theobromae, causal agent of vascular streak dieback (VSD), from cacao stems showing symptoms of VSD, 74% of recovered fungi were Lasiodiplodia spp. A phylogenetic tree generated for 52 Lasiodiplodia isolates based on the partial rDNA and EF1a gene sequences indicates that at least three different Lasiodiplodia spp. are associated with the cacao in South East Asia. Lasiodiplodia isolates showed intra and interspecific variation in virulence when assayed using cacao leaf discs. The current study reports on the 43.75 Mb de novo assembled genome of a Ltheo isolate from cacao. Ab initio gene prediction has generated 13,061 protein-coding genes, of which 2,862 are unique to Ltheo, when compared to other closely related Botryosphaeriaceae fungi. Transcriptome analysis revealed that 11,860 predicted genes were transcriptionally active and 1,255 were induced in planta compare to cultured mycelia. The predicted genes induced during infection were mainly those involved in carbohydrate, pectin and lignin catabolism, cytochrome P450s, necrosis-inducing proteins and putative effectors. These findings significantly expand our knowledge of the Ltheo genome and Ltheo genes involve in virulence and pathogenicity, and the Ltheo infection process in cacao.