The poplar pangenome provides insights into the evolutionary history of the genus

The genus Populus comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus Populus , identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism–structural variation (SNP–SV) density and indel–SV density to complement the SNP–indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.