Phylogenomic and single nucleotide polymorphism analyses revealed the hybrid origin of Spondias bahiensis (family Anacardiaceae): de novo genome sequencing and comparative genomics

Abstract The genus Spondias (family Anacardiaceae) comprises 19 taxa, ten of which occur in Neotropical regions. Spondias bahiensis has been suggested to be a hybrid, although initial evidence does not support this hypothesis. The aim of this study was to test the hypothesis of the hybrid origin of S. bahiensis using high-throughput sequencing with single nucleotide polymorphism (SNP) analysis, characterization of intragenomic nuclear ribosomal DNA (nrDNA), and nuclear and chloroplast phylogenomic analyses. The SNP analysis revealed a high number of SNPs in the S. bahiensis genome, and with respect to nrDNA, S. bahiensis shared approximately half of the SNP alleles with S. tuberosa, but not with S. mombin. Combining the SNP analysis with nrDNA phylogeny confirmed the hybrid origin of S. bahiensis and put S. tuberosa as the female genitor. Considering the phylogeny of the genus Spondias and intraspecific SNPs in S. bahiensis, the putative male genitor is S. dulcis.