Mendieta John Pablo, Tu Xiaoyu, Jiang Daiquan, Yan Haidong, Zhang Xuan, Marand Alexandre P, Zhong Silin, Schmitz Robert J
Department of Genetics, University of Georgia.
Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
bioRxiv. 2024 May 16:2024.01.05.574340. doi: 10.1101/2024.01.05.574340.
While considerable knowledge exists about the enzymes pivotal for C photosynthesis, much less is known about the -regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C enzymes for five different grass species. This study spans four C species, covering three distinct photosynthetic subtypes: and (NADP-ME), (NAD-ME), (PEPCK), along with the C outgroup . We studied the -regulatory landscape of enzymes essential across all C species and those unique to C subtypes, measuring cell-type-specific biases for C enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C evolution. Besides promoter proximal ACRs, we found that, on average, C genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution of -regulation at these C loci. This study illuminates the dynamic and complex nature of CRE evolution in C photosynthesis, particularly highlighting the intricate -regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C crop performance under changing climatic conditions.
虽然我们对C4光合作用关键酶已有相当多的了解，但对于决定这些酶在不同细胞类型中表达的调控机制却知之甚少。在这里，我们使用单细胞索引ATAC-seq来识别与五种不同禾本科植物C4酶相关的细胞类型特异性可及染色质区域（ACR）。本研究涵盖了四种C4植物，包括三种不同的光合亚型：NADP-ME、NAD-ME、PEPCK，以及C3外类群。我们研究了所有C4植物共有的必需酶以及C4亚型特有的酶的调控格局，利用染色质可及性数据测量C4酶的细胞类型特异性偏差。将这些数据与系统发育学相结合，揭示了物种间基因家族成员的多样化共选择，展示了C4进化的多种路径。除了启动子近端ACR，我们发现，平均而言，C4基因有两到三个远端细胞类型特异性ACR，突出了C4进化的复杂性和多样性。对这些细胞类型特异性ACR的进化历史进行研究发现，即使在亲缘关系密切的物种之间，也存在一系列保守和新颖的ACR，这表明这些C4位点的调控正在不断进化。这项研究揭示了C4光合作用中CRE进化的动态和复杂本质，尤其突出了关键位点复杂的调控进化。我们的发现为未来的研究提供了宝贵的资源，可能有助于在不断变化的气候条件下优化C4作物的性能。
