Three Novel Genomes Broaden the Wild Side of the <i>Capsicum</i> Pangenome

This study presents three genome assemblies within the <i>Capsicum</i> genus, enabling comprehensive comparative analyses for the <i>Annuum</i> and <i>Baccatum</i> complexes within the genus. We produced highly continuous assemblies of the nuclear genomes and complete chloroplast assemblies. Subsequent genome annotation identified 34,580 genes in nonpungent <i>C. annuum</i> cv. ECW, and 32,704 and 33,994 genes in pungent <i>C. chacoense</i> and <i>C. galapagoense</i>, respectively. These assemblies, including the first complete genomes for <i>C. chacoense</i> and <i>C. galapagoense</i>, provide additional genomic resolution within the <i>Capsicum</i> genus. The novel genomes were analyzed within a pangenomic framework, integrating 16 <i>Capsicum</i> genomes across the <i>Annuum</i>, <i>Baccatum</i>, and <i>Pubescens</i> complexes. Homology grouping was used to identify core, accessory and unique genes and showed a wide spectrum of genetic diversity, particularly in homology groups exclusive to <i>C. chacoense</i> and <i>C. galapagoense</i>. Out of 79,267 homology groups identified, 13% were core groups, present in all accessions, corresponding to approximately 30% of core genes per genome. Comparative analyses revealed distinct species and genus-specific genomic characteristics. Additionally, we used the graph pangenome to illustrate locus-level exploration by examining the <i>Pun1</i> locus associated with capsaicinoid biosynthesis, identifying multiple <i>Pun1</i>-like genes including their genomic position and homology information. The integration of these new resources into a dynamic <i>Capsicum</i> pangenome framework provides a versatile platform for extracting genetic information relevant to both fundamental research and breeding applications.