Supporting data for "Chromosome-Level Genome Assembly of <i>Pinus massoniana</i> provides insights into Conifer Adaptive Evolution"
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<i>Pinus massoniana</i>, a conifer of significant economic and ecological value in China, is renowned for its wide adaptability and oleoresin production. We sequenced and assembled the chromosomal-level <i>P. massoniana</i> genome, revealing 80,366 protein-coding genes and significant gene family expansions associated with stress response and plant-pathogen interactions. Long-intron genes, which are predominantly presented in low-copy gene families, are strongly linked to the recent LTR burst in the <i>Pinus</i> genome. By reanalyzing population transcriptomic data, we identified genetic markers linked to oleoresin synthesis, including those within the <i>CYP450</i> and <i>TPS</i> gene families. The results suggest that the genes of resin terpene biosynthesis pathway can be activated in several cell types and the oleoresin yield may depend on the rate-limiting enzymes. <br>Using a multi-omics algorithm, we identified several regulatory factors, including PmMYB4 and PmbZIP2, that interact with <i>TPS</i> and <i>CYP450</i> genes, potentially playing a role in oleoresin production. This was further validated through molecular genetics analyses. We observed signatures of adaptive evolution in dispersed duplicate and horizontal gene transfer events that have contributed to the species adaptation. This study provides insights for further research into the evolutionary biology of conifers and lays the groundwork for genomic-assisted breeding and sustainable management of Masson pine.
马尾松（Pinus massoniana）是中国兼具重要经济与生态价值的针叶树种，以广泛的环境适应性与松脂生产能力闻名。本研究对其完成了染色体级全基因组测序与组装，共注释得到80366个蛋白质编码基因，并发现与胁迫响应、植物-病原体互作相关的基因家族发生了显著扩张。主要分布于低拷贝基因家族的长内含子基因，与松属基因组近期发生的LTR（长末端重复序列）爆发存在显著关联。通过重新分析群体转录组数据，我们鉴定出一批与松脂合成相关的遗传标记，涵盖CYP450与TPS基因家族。研究结果显示，松脂萜类生物合成通路的基因可在多种细胞类型中被激活，松脂产量或取决于限速酶的活性。 我们借助多组学算法，鉴定出包括PmMYB4与PmbZIP2在内的多个调控因子，这些因子可与TPS、CYP450基因相互作用，在松脂生成过程中发挥潜在调控功能，该结论经分子遗传学分析进一步得到验证。本研究还观察到，在散在重复基因与水平基因转移事件中存在适应性进化特征，这些演化事件推动了马尾松的物种适应性形成。本研究为针叶树进化生物学的后续研究提供了重要见解，同时为马尾松的基因组辅助育种与可持续经营奠定了坚实的理论基础。
