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）相较于祖先型C3光合作用，在各类自然与农业生态系统中均表现更优，因其具备更高的水分利用效率与氮素利用效率。因此，通过将该性状引入C3遗传背景中，C4光合作用可作为培育新型高产作物的核心靶点。然而，C4光合作用的遗传结构目前仍未被充分解析。为解析叶片发育过程中C3与C4光合作用相关基因表达模块的差异，本研究通过RNA测序（RNA sequencing）构建了两株山柑科物种的全面转录组图谱：Gynandropsis gynandra（C4型）与Tarenaya hassleriana（C3型）。整体而言，C3与C4物种的基因表达谱极为相似。研究发现，已知的C4功能基因从C3物种的不同表达结构域被招募至光合通路中，涵盖各类组织中的典型持家基因（housekeeping gene）表达模式，以及特定的异养组织表达模式。此外，本研究还鉴定出一个从C3物种根系招募而来的结构相关基因模块。通过对比叶片发育过程中的基因表达模式与解剖结构特征，本研究深入解析了花环结构（Kranz anatomy）的遗传特征。发育因子与细胞周期基因的表达改变，与C4植物肿大的维管束鞘细胞中更高程度的核内复制密切相关。叶片解剖结构与转录组均显示出的叶肉细胞分化延迟，使得C4植物叶片能够延长叶脉形成过程。