The chromosome-scale genome of the drought-adapted Caatinga tree Spondias tuberosa reveals a conserved, unduplicated architecture within Anacardiaceae

Spondias tuberosa (umbu) is a tree endemic to the semi-arid Caatinga of north-eastern Brazil, adapted to recurrent drought and high temperatures. Although genomes of mango (Mangifera indica), pistachio (Pistacia vera) and cashew (Anacardium occidentale) are available, comparative analyses of genome evolution across Anacardiaceae remain scarce. We aimed to generate a chromosome-scale reference genome for S. tuberosa and use it to examine genome architecture, meiotic recombination and gene family evolution within the family. We assembled the genome of a single individual using PacBio HiFi and Omni-C (Hi-C) data, mapped meiotic crossovers by single-nucleus RNA sequencing of pollen, and compared the genome with those of six other Sapindales species through orthology, synteny, synonymous substitution (Ks) and gene family expansion/contraction analyses within a dated phylogenomic framework. The assembly anchors 288 Mb onto 16 chromosomes (98.8% BUSCO completeness) and contains 24,232 protein-coding genes, 52.01% repetitive DNA and 1.78 million heterozygous SNPs (0.62%). We identified 1,740 crossovers in 153 pollen nuclei (4.01 cM.Mb1), which were depleted in repeat-rich pericentromeric regions. Ks analyses revealed a whole-genome duplication shared by Mangifera and Anacardium that is absent from S. tuberosa, which retains only the ancient γ triplication. The 97 gene families expanded in S. tuberosa, mostly through tandem duplication, include receptor-like kinases, glutathione S-transferases and disease-resistance proteins, consistent with roles in environmental sensing and stress tolerance. Genome structure has remained highly conserved across Sapindales, except in the mango cashew lineage, which underwent extensive rearrangements following a whole-genome duplication. As sister to the remaining Anacardiaceae sampled and with an unduplicated, largely collinear architecture, S. tuberosa provides a reference for comparative mapping and for transferring genomic information to economically important woody relatives.