Haplotype-resolved assembly and resequencing analysis highlight crucial components of pine genome evolution and allelic imbalance in Pinus densiflora. Pinus densiflora

Haplotype-level allelic characterization facilitates research on the functional, evolutionary, and breeding-related features of extremely large and complex plant genomes. We report the 21.7 Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosome 1 and 3 of Pinus species, and a proliferation of specific long terminal repeat-retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT mediated duplications led to a remarkable increment of transcription factors (TFs) in P. densiflora. Comparison of P. densiflora haplotypes A and B uncovered allelic imbalances, including presence absence variations of genes (PAV genes), and their functional contributions to P. densiflora traits. Allele-aware resequencing analysis unveiled the allele and PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs, and TF genes within Pinus lineage, as well as allelic imbalances and diversity across P. densiflora.