Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species

C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C4) and Tarenaya hassleriana (C3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C3 and C4 species. We found that known C4 genes were recruited to photosynthesis from different expression domains in C3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C4 leaf.

C4光合作用（C4 photosynthesis）在多种自然与农业生态系统中均优于祖先型C3状态，因其具备更高的水分利用效率与氮素利用效率。因此，通过将C4光合性状引入C3作物遗传背景以培育新型高产作物，C4光合作用成为极具潜力的靶标性状。然而，目前C4光合作用的遗传结构仍未被充分解析。
为明确叶片发育过程中C3与C4光合作用之间的基因表达模块差异，我们通过RNA测序（RNA sequencing）构建了两个白花菜科（Cleomaceae）物种的全面转录组图谱：四棱白花菜（Gynandropsis gynandra，C4型）与醉蝶花（Tarenaya hassleriana，C3型）。
总体而言，C3与C4物种的基因表达谱呈现出极高的相似性。我们发现，已知的C4光合基因从C3物种的不同表达结构域中被招募至光合通路中，包括各类组织中典型的持家基因表达模式，以及特定的异养组织表达模式。此外，我们还鉴定出一个从C3物种根系招募而来的结构相关基因表达模块。
通过比对叶片发育过程中的基因表达模式与解剖结构特征，我们深入解析了花环型解剖结构（Kranz anatomy）的遗传调控特征。发育调控因子与细胞周期基因的表达改变，与膨大的C4维管束鞘细胞中更高程度的核内复制密切相关。无论是在叶片解剖结构还是转录组层面，均观察到叶肉分化延迟的现象，这使得C4叶片的叶脉形成过程得以延长。