Chromosome-level haplotype-resolved genome assembly of 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.
<br>
HaplotypeA - P.densiflora_v1.0_HA
HaplotypeB - P.densiflora_v1.0_HB
Variation_information_of_P.densiflora_accessions.txt.gz : Genotype information generated from resequencing analysis of P. densiflora accessions

单倍型水平的等位基因特征解析，可为超大型复杂植物基因组的功能、进化及育种相关特征研究提供助力。本研究报道了赤松（Pinus densiflora）21.7 Gb染色体级单倍型解析组装体。研究发现，松属物种的1号与3号染色体间存在涉及易位和倒位的基因组重排，且赤松中存在特异性长末端重复序列反转录转座子（long terminal repeat-retrotransposons, LTR-RTs）的大量扩增。进化分析表明，串联重复与LTR-RT介导的复制事件导致赤松中转录因子（transcription factors, TFs）数量显著提升。对赤松单倍型A与单倍型B的比较揭示了等位基因失衡现象，包括基因有无变异（presence absence variations of genes, PAV基因）及其对赤松性状的功能贡献。等位基因知晓式重测序分析揭示了赤松种质间的等位基因及PAV基因多样性。本研究为松属谱系内基因组结构、LTR-RTs及TF基因进化的关键机制，以及赤松的等位基因失衡与多样性提供了重要见解。
单倍型A — 赤松_v1.0_HA
单倍型B — 赤松_v1.0_HB
赤松种质变异信息.txt.gz：该文件为赤松种质重测序分析得到的基因型信息

搜集汇总

背景与挑战

背景概述

该数据集提供了赤松(Pinus densiflora)21.7 Gb染色体级别单倍型解析基因组组装结果，包含两个单倍型(HA和HB)的比较分析，揭示了基因组重排、转座子扩增和转录因子扩张等进化特征，并提供了赤松种质的等位基因多样性信息。