The baldcypress genome provides insights into the adaptive evolution of flooding stress tolerance

● The evolutionary history of gymnosperms suggests that most species struggle in wet environments. However,, baldcypress (<i>Taxodium distichum</i><i> </i>var. <i>distichum</i>) thrives in wetlands,, making it a prime candidate for studying flood tolerance in gymnosperms. Our study aimed to explore the genetic basis of this flood tolerance.● We accomplished the first chromosome-level genome assembly of baldcypress. Using <i>Oryza sativa</i>, <i>Arabidopsis thaliana</i>, baldcypress, and <i>Taxus wallichiana</i>, we compared gene expression, regulatory elements, and gene expansions between flood-tolerant and flood-intolerant plants.● The baldcypress genome spans approximately 7.82 Gb, containing 44,010 protein-coding genes. We identified 409 commonly upregulated and 668 commonly downregulated orthogroups, representing conserved flood-stress responses. Additionally, 352 orthogroups contained more upregulated genes in tolerant plants. Baldcypress appears to employ different evolutionary strategies than rice to withstand flooding. Both strategies involve the evolution of ERF-VII transcriptional activation and antioxidant pathways. However, each species expanded distinct nodes within these pathways. Additionally, the evolution of spliceosome genes in baldcypress and energy-producing genes in rice further reflects their differing evolutionary strategies.● This study underscores the diversity and commonality of mechanisms underlying plant flood responses and tolerance, providing theoretical guidance for research on the genetic improvement of plant flooding tolerance.

● 裸子植物的演化历史表明，多数物种难以在湿润环境中存活。但落羽杉（*Taxodium distichum* var. *distichum*）却能在湿地中蓬勃生长，成为研究裸子植物耐涝性的理想候选材料。本研究旨在探究其耐涝性的遗传基础。
● 我们首次完成了落羽杉的染色体级基因组组装。本研究选取水稻（*Oryza sativa*）、拟南芥（*Arabidopsis thaliana*）、落羽杉以及云南红豆杉（*Taxus wallichiana*）作为研究材料，对比了耐涝与不耐涝植物的基因表达、调控元件以及基因扩张特征。
● 落羽杉基因组总长约7.82 Gb，共包含44010个蛋白质编码基因。我们鉴定得到409个共同上调同源基因簇（orthogroup）与668个共同下调同源基因簇，它们代表了保守的涝胁迫响应机制。此外，有352个同源基因簇在耐涝植物中存在更多上调表达的基因。落羽杉应对涝胁迫的演化策略与水稻存在显著差异。二者均通过演化乙烯响应因子VII（ERF-VII）转录激活途径与抗氧化通路实现耐涝，但各自在这些通路中扩张了不同的功能节点。此外，落羽杉剪接体基因的演化与水稻能量产生相关基因的演化，进一步体现了二者迥异的演化策略。
● 本研究阐明了植物涝响应与耐涝机制的多样性与共性，为植物耐涝性的遗传改良研究提供了重要的理论指导。