Data_Sheet_1_StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication.PDF

The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.

类固醇生成急性调节蛋白（StAR）相关脂质转运（START）结构域包含蛋白（简称START蛋白）由植物中扩增的进化保守基因家族编码，在植物界中参与脂质结合、脂质转运、信号转导及转录活性调控，但目前关于其进化、基因复制以及伴随的亚功能化或新功能化的相关研究信息仍较为匮乏。本研究针对水稻泛基因组中的该基因家族，利用10份野生及栽培稻品种开展了全面的系统性研究。对10份水稻基因组中START结构域的保守性分析显示，该家族成员的必需性较低且发挥关键功能，这一结论进一步得到染色体定位、基因复制事件及结构域组成模式的佐证。共线性分析显示，START家族基因的复制以片段复制和弥散复制为主；针对主要栽培品种粳稻（Oryza sativa var. japonica）的转录组分析表明，该家族成员在不同发育阶段及组织（如花器官）中存在显著的表达偏好性，印证了亚功能化现象。非同义替换率与同义替换率的比值（Ka/Ks）分析证实，START家族在进化过程中受到强烈的纯化选择（负选择）作用，表明水稻驯化过程中的选择压力在个体发育进程中得以重演。本研究结果证实，不同水稻品种间START基因在数量及Ka/Ks比值的严格调控上均保持高度保守，同时表明植物的生长与生殖发育高度依赖START蛋白的功能。我们认为本研究结果拓展了学界对植物START结构域多样性与进化的有限认知，为后续深入解析植物中不同结构类别的START蛋白及其结构域特异性底物偏好性奠定了基础，以补充现有动物与酵母中的相关研究成果。