Genome and transcriptome analysis of the latent pathogen Lasiodiplodia theobromae, an emerging threat to the cacao industry

Abstract

<i>Lasiodiplodia theobromae</i> (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. While attempting to isolate <i>Ceratobasidium theobromae</i>, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were <i>Lasiodiplodia</i> spp. Sequence-based identification of 52 putative isolates of <i>L. theobromae</i> indicated that diverse species of <i>Lasiodiplodia</i> were associated with cacao in the studied areas, and the isolates showed variation in aggressiveness when assayed using cacao leaf discs. The present study reports a 43.75 Mb de novo assembled genome of an isolate of <i>L. theobromae</i> from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to <i>L. theobromae</i>, when compared with other closely related Botryosphaeriaceae. Transcriptome analysis revealed that 11 860 predicted genes were transcriptionally active and 1255 were more highly expressed in planta compared with cultured mycelia. The predicted genes differentially expressed during infection were mainly those involved in carbohydrate, pectin, and lignin catabolism, cytochrome P450, necrosis-inducing proteins, and putative effectors. These findings significantly expand our knowledge of the genome of <i>L. theobromae</i> and the genes involved in virulence and pathogenicity.

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