The Genome of Eleocharis vivipara Elucidates the Genetics of C3-C4 Photosynthetic Plasticity and Karyotype Evolution in the Cyperaceae.

Eleocharis vivipara, an amphibious plant in Cyperaceae family, was reported to have numerous valuable biological traits, particularly its adaptive photosynthesis plasticity that employing C3 type underwater and C4 type on land. However, the evolutionary and genetic studies of it have been hampered due to lack of genomes. Here we assembled a high-quality genome of E. vivipara, the first chromosome-level genome of Eleocharis genus, with its size ~965.22 Mb and contains 10 chromosomes. Its diagonal Hi-C pattern for adjacent chromosomes, and its 1-to-1 genome synteny relationship for two subgroups suggested it is a tetraploid with n = 2x = 10. Phylogeny result displayed the Eleocharis diverged with Cyperus genus ~23.11 Mya, a closer relationship than others in Cyperaceae. Interestingly, the well 1-to-1 genome synteny result for the subgenome 2 of E. vivipara (x = 5), the genomes of Cyperus esculentus (n = 54) and Rhynchospora tenuis (n = 2), displayed twice chromosomes fusion events resulted to their number reduction from 54 to 5 and then to 2. Compared with its close relative Juncus effusus which has monocentromeres, we found E. vivipara showed characteristics of holocentromeres that can maintain the stability of its fusion chromosomes. Strikingly, transplanting experiment displayed its culms anatomy gradually presented Proto-Kranz structure with increased number of chloroplasts in BS cells in terrestrial culms. Further comparison results not only displayed most of its C4 photosynthesis related genes showed higher expression, but also identified 2,602 up-DEGs that mainly functional in response to water deprivation and ABA, revealed the drought inducted transition of C4 photosynthesis in E. vivipara. Briefly, our results not only shed light on the karyotype evolution of Cyperaceae, but also provided new valuable insights into C3 and C4 transformation that will benefit for crop improvement and breeding.

胎生荸荠（Eleocharis vivipara）是莎草科（Cyperaceae）的两栖植物，据报道其具备多项极具价值的生物学特性，尤其是其适应性光合可塑性：水下环境下采用C3光合途径，陆地环境则切换为C4光合途径。然而，由于缺乏参考基因组，针对该物种的演化与遗传学研究长期受阻。本研究组装获得了胎生荸荠的高质量基因组，这是荸荠属（Eleocharis）首个染色体级别的参考基因组，基因组大小约为965.22 Mb，包含10条染色体。相邻染色体的高通量染色体构象捕获（Hi-C）图谱呈对角线分布，结合两个亚组间的1对1基因组共线性关系，均可证明该物种为四倍体，其染色体基数为n = 2x = 10。系统发育分析结果显示，荸荠属与莎草属（Cyperus）的分化时间约为23.11百万年前，二者的亲缘关系相较于莎草科其他类群更为紧密。值得注意的是，通过对胎生荸荠第二亚基因组（x=5）、油莎草（Cyperus esculentus，n=54）以及细穗刺子莞（Rhynchospora tenuis，n=2）的高质量1对1基因组共线性分析，结果显示二者历经两次染色体融合事件，使得染色体数目从54逐步缩减至5，最终变为2。与其具有单着丝粒的近缘物种灯心草（Juncus effusus）相比，本研究发现胎生荸荠具备全着丝粒特征，该特征可有效维持其融合染色体的结构稳定性。尤为引人注目的是，移栽实验结果显示，陆生茎秆的解剖结构逐渐呈现出原Kranz结构，且其维管束鞘（BS）细胞内的叶绿体数量显著提升。进一步的比较分析结果显示，该物种绝大多数C4光合相关基因的表达水平显著上调，同时还鉴定得到2602个上调差异表达基因（up-DEGs），这些基因主要参与水分胁迫应答与脱落酸（ABA）信号通路，揭示了干旱诱导胎生荸荠发生C4光合途径转变的分子机制。综上，本研究结果不仅为莎草科的核型演化研究提供了全新视角，同时也为C3与C4光合途径的转化机制研究提供了宝贵的新见解，将为作物遗传改良与育种工作提供重要支撑。