A gap-free reference genome of Populus deltoides provides insights into karyotype evolution of Salicaceae.

Abstract

Background: As a species of poplar with significant economic and ecological value, the high-quality genome assembly of Populus deltoides (P. deltoides) is crucial for understanding its growth and development, stress resistance, and biosynthetic pathways.

Results: We presented a gap-free telomere-to-telomere (T2T) assembly of the P. deltoides genome using PacBio HiFi and Hi-C sequencing data. The P. deltoides genome is 395.9 Mb in length and consists of 27 contigs (contig N50: 22.73 Mb), encompassing nearly all telomeres (36 out of 38). Following careful evaluations of genome accuracy and completeness, our assembly represents a substantial enhancement over the previously published genomes of P. deltoides, eliminating all gaps and rectifying numerous assembly errors. The expanded and contracted gene families of the P. deltoides genome were significantly enriched in functions crucial for stress and defense responses, as well as environmental adaptation. Additionally, our study confirms that all Salicaceae genomes have undergone at least two major whole genome duplication events. The most recent duplication event, shared by between Salicaceae and Manihot esculenta, is estimated to have occurred approximately 44.2 to 57.8 Mya. Most importantly, we reconstructed the ancestral karyotype of Salicaceae, which comprised 11 proto-chromosomes.

Conclusions: This study provides strong evidence for comprehensive understanding of the evolutionary dynamics within Salicaceae genomes and provides valuable genomic resources for the genetic improvement and biological breeding of P. deltoides.