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Lasiodiplodia theobromae (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 Ceratobasidium theobromae, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were Lasiodiplodia spp. Sequence-based identification of 52 putative isolates of L. theobromae indicated that diverse species of Lasiodiplodia 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 L. theobromae from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to L. theobromae, 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 L. theobromae and the genes involved in virulence and pathogenicity. Keywords: cacao, Lasiodiplodia, genome, transcriptome, effectors. Le Lasiodiplodia theobramae (Pat.) Griffon & Maubl., un membre de la famille des Botryosphaeriaceae, est en train de devenir une menace importante chez plusieurs cultures et especes ligneuses dans plusieurs regions du monde, incluant les regions productrices de cacaoyer. En tentant d'isoler le Ceratobasidium theobromae, l'agent causal du deperissement avec necrose vasculaire (VSD), a partir de tiges symptomatiques, 74 % des champignons isoles appartenaient aux Lasiodiplodia spp. Une identification moleculaire de 52 isolats putatifs du Lasiodiplodia a permis de montrer que diverses especes de Lasiodiplodia etaient associees au cacaoyer dans les regions etudiees et que ces isolats montraient une agressivite variable lorsque celle-ci etait mesuree sur des disques foliaires. La presente etude rapporte un genome de 43,75 Mb assemble de novo a partir d'un isolat L. theobromae du cacaoyer. Une prediction de genes ab initio a produit 13 061 genes codant pour des proteines, dont 2862 etaient uniques au L. theobromae par rapport a d'autres Botryosphaeriaceae. Une analyse transcriptomique a revele que 11 860 des genes predits etaient transcrits et que 1255 de ceux-ci etaient plus fortement exprimes in planta que chez le mycelium en culture. Les genes predits qui etaient exprimes de maniere differentielle au cours de l'infection etaient principalement ceux impliques dans le catabolisme des hydrates de carbone, de la pectine et de la lignine, ainsi que des cytochromes P450, des proteines induisant la necrose et des effecteurs putatifs. Ces resultats accroissent significativement nos connaissances sur le genome ainsi que les genes du L. theobromae que sont impliques dans la virulence et la pathogenicite. [Traduit par la Redaction] Mots-cles : cacaoyer, Lasiodiplodia, genome, transcriptome, effecteurs., Introduction Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is often considered a latent plant pathogen attacking more than 500 plant species in the tropics and [...]