PT  - JOURNAL ARTICLE
AU  - Winters, Noah P.
AU  - Wafula, Eric K.
AU  - Timilsena, Prakash R.
AU  - Ralph, Paula E.
AU  - Maximova, Siela N.
AU  - de Pamphilis, Claude W.
AU  - Guiltinan, Mark J.
AU  - Marden, James H.
TI  - Local Gene Duplications Drive Extensive NLR Copy Number Variation Across Multiple Genotypes of <em>Theobroma cacao</em>
AID  - 10.1101/2024.09.01.610724
DP  - 2024 Jan 01
TA  - bioRxiv
PG  - 2024.09.01.610724
4099  - http://biorxiv.org/content/early/2024/09/03/2024.09.01.610724.short
4100  - http://biorxiv.org/content/early/2024/09/03/2024.09.01.610724.full
AB  - Nucleotide-binding leucine rich repeat receptors (NLR) are an essential component of plant immunity. NLR evolution is complex and dynamic, with rapid expansions, contractions, and polymorphism. Hundreds of high-quality plant genomes generated over the last two decades provide substantial insight into the evolutionary dynamics of NLR genes. Despite steadily decreasing sequencing costs, the difficulty of sequencing, assembling, and annotating high-quality genomes has resulted in comparatively little genome-wide information on intraspecies NLR diversity. In this study, we investigated the evolution of NLR genes across 11 high-quality genomes of the chocolate tree, Theobroma cacao L. We found 3-fold variation in NLR copy number across genotypes, a pattern driven primarily by expansion of NLR clusters via tandem and proximal duplication. Our results indicate local duplications can radically reshape gene families over short evolutionary time scales, creating extensive intraspecific variation and a source of NLR diversity that could be utilized to enrich our understanding of both plant-pathogen interactions and resistance breeding.Competing Interest StatementThe authors have declared no competing interest.