ArticleThe plant genome2026
Integrative chromosome-scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma.
Article in The plant genome, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
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9 authors.
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Abstract
Cupuassu (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.
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