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.

摘要 槟榔青属（*Spondias*，漆树科（Anacardiaceae））共计19个类群，其中10个类群分布于新热带区。此前有研究提出巴哈槟榔青（*Spondias bahiensis*）为杂交起源，但初始证据并不支持这一假说。本研究旨在通过高通量测序结合单核苷酸多态性（single nucleotide polymorphism, SNP）分析、基因组内核糖体DNA（nuclear ribosomal DNA, nrDNA）的特征解析，以及核基因组与叶绿体基因组系统基因组学分析，验证巴哈槟榔青的杂交起源假说。SNP分析结果显示，巴哈槟榔青基因组中存在大量SNP位点；针对nrDNA的分析表明，巴哈槟榔青与块根槟榔青（*S. tuberosa*）共享约半数的SNP等位基因，而与茂物槟榔青（*S. mombin*）并无此类共享。结合SNP分析与nrDNA系统发育结果，证实了巴哈槟榔青的杂交起源，并确定块根槟榔青为其母本亲本。综合槟榔青属的系统发育关系与巴哈槟榔青的种内SNP特征，推测其雄性亲本为甜槟榔青（*S. dulcis*）。