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. Bingyu Zhang et al. present the pan-genome of Chinese poplars, finding millions of sequence and structural variations and an expansion of disease resistance genes among genes with heterozygous non-functioning variations. They also find evidence of genomic control of self-fertilization in poplar.