Integrative chromosome‐scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma.

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dc.contributorVINICIUS A. C. DE ABREU, UNIVERSIDADE FEDERAL DO PARÁ; RAFAEL MOYSES ALVES, CPATU; MAURO DE MEDEIROS OLIVEIRA, UNIVERSIDADE ESTADUAL PAULISTA; VITOR TRINCA, UNIVERSIDADE ESTADUAL PAULISTA; LOENI LUDKE FALCAO, CENARGEN; LUCILIA HELENA MARCELLINO, CENARGEN; ANTONIO FIGUEIRA, UNIVERSIDADE DE SÃO PAULO; DOUGLAS S. DOMINGUES, UNIVERSIDADE DE SÃO PAULO; ALESSANDRO M. VARANI, UNIVERSIDADE ESTADUAL PAULISTA.
dc.creatorABREU, V. A. C. de
dc.creatorALVES, R. M.
dc.creatorOLIVEIRA, M. de M.
dc.creatorTRINCA, V.
dc.creatorFALCAO, L. L.
dc.creatorMARCELLINO, L. H.
dc.creatorFIGUEIRA, A.
dc.creatorDOMINGUES, D. S.
dc.creatorVARANI, A. M.
dc.date2026-03-06T17:11:05Z
dc.date2026-03-06T17:11:05Z
dc.date2026-03-06
dc.date2026
dc.date.accessioned2026-06-30T23:54:58Z
dc.descriptionCupuassu (Theobroma grandiflorum) is a fruit tree native to the Brazilian Amazon and increasingly relevant to regional bioeconomies. Its cultivation is severely affected by witches’ broom disease (WBD), caused by Moniliophthora perniciosa. While a chromosome-scale genome of the susceptible genotype C1074 is available, the lack of a resistant reference has limited investigation into the genomic basis of resistance. Here, we present the first chromosome-scale assembly of the WBD-resistant genotype C174 (415.8 Mb) and a comparative analysis with C1074 integrating structural variant detection, gene-duplication profiling, transposable-element (TE) annotation, and time-resolved host–pathogen transcriptomics. C174 exhibits distinctive tandem and dispersed duplications, genotype-specific TE insertions, and coordinated defense-gene expression, together with higher heterozygosity indicative of broader allelic diversity. Genome-wide, TEs show differential expression and spatial proximity to immune loci, suggesting potential regulatory importance. Although C1074 encodes more nucleotide-binding domain leucine-rich repeat receptors (541 vs. 434), most remain transcriptionally inactive, whereas C174 shows sequential activation of pattern-recognition receptors, mitogen-activated protein kinase components, transcription factors, and pathogenesis-related proteins. Within the Chromosome 6 previously identified resistance quantitative trait locus, two duplicated DUF4220/DUF594 genes (where DUF is domain of unknown function) unique to C174—orthologous to a maize gene implicated in fungal response before—are infection-induced and display signatures of episodic positive selection. Together, these results establish a high-quality genomic framework for exploring the molecular architecture of WBD response in T. grandiflorum. The datasets generated here—including the C174 and C1074 reference genomes, immune-related variant catalog, and prioritized defense-gene lists—constitute a comprehensive open resource for evolutionary, functional, and breeding research of Theobroma species.
dc.identifierThe Plant Genome, v. 19, n. 1, e70196, 2026.
dc.identifier1940-3372.
dc.identifierhttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1185135
dc.identifierhttps://doi.org/10.1002/tpg2.70196
dc.identifier.urihttp://hdl.handle.net/123456789/393156
dc.languageeng
dc.rightsopenAccess
dc.subjectCupuaçu
dc.subjectTheobroma Grandiflorum
dc.subjectDoença
dc.subjectDoença de Planta
dc.subjectVassoura de Bruxa
dc.subjectResistência
dc.subjectGenoma
dc.titleIntegrative chromosome‐scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma.
dc.typeArtigo de periódico

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