Supplementary Information: RNA-Seq analysis of Brassicaceae species under different irradiances

This package contains supplementary information supporting conclusions from an RNA-Seq experiment conducted on Brassicaceae species grown under different irradiances. In this study, co-authors and I aimed to comprehend the genetic and physiological underpinnings of photosynthetic light-use efficiency (LUE) under high irradiance conditions, focusing on the plant species <em>Hirschfeldia incana</em>. We performed a comparison of the transcriptional signature associated to very high, "supernatural" irradiance in <em>H. incana </em>with three other Brassicaceae plants (<em>Arabidopsis thaliana</em>, <em>Brassica rapa</em>, and <em>Brassica nigra</em>), which previously demonstrated lower photosynthetic LUE. By utilizing a panproteome, we assessed gene expression patterns in response to high irradiance across the four species. Our findings reveal that all species actively regulate genes linked to photosynthesis. Analyzing genes associated with three key photosynthetic pathways, we observed a consistent pattern of reduced gene expression under high irradiance conditions. Notably, specific genes exhibited differential expression exclusively in <em>H. incana</em>, while in other instances, transcript abundance was consistently higher in<em> H. incana </em>regardless of light intensity. In conclusion, the study this software supports presents the first comparative transcriptome analysis of plant species grown entirely under prolonged high irradiance, rather than just briefly exposed to it. We demonstrate that, in contrast to other Brassicaceae species, <em>H. incana </em>subjected to intense irradiance displays enhanced gene expression related to photosynthesis through distinct mechanisms: canonical differential expression, inherent elevated expression of single-copy genes, and cumulative elevated expression via simultaneous expression of multiple gene copies. This research establishes a crucial groundwork for future endeavors aimed at comprehending elevated photosynthetic light-use efficiency and ultimately achieving highly effective photosynthesis in agricultural crops.

本数据包包含支撑一项RNA测序（RNA-Seq）实验结论的补充信息，该实验以不同光照强度下培育的十字花科（Brassicaceae）物种为研究对象。本研究中，笔者与合著者旨在解析高光强条件下光合光利用效率（LUE）的遗传与生理基础，研究重点为*Hirschfeldia incana*这一植物物种。我们将*H. incana*在极高（“超自然”）光照强度下的转录特征，与另外3种此前被证实光合光利用效率偏低的十字花科植物——*拟南芥（Arabidopsis thaliana）*、*芜菁（Brassica rapa）*和*黑芥（Brassica nigra）*——进行了比较分析。本研究借助泛蛋白质组（panproteome）技术，评估了4个物种在响应高光强时的基因表达模式。研究结果显示，所有受试物种均会主动调控与光合作用相关的基因。通过对3条核心光合通路相关基因的分析，我们发现高光强条件下这些基因的表达量普遍呈现下降趋势。值得注意的是，部分基因仅在*H. incana*中出现差异表达；而在其他场景下，无论光照强度如何，*H. incana*的转录本丰度始终高于其他物种。综上，本数据包所支撑的这项研究，首次对长期处于高光强环境（而非短暂高光暴露）下的植物物种开展了比较转录组分析。我们证实，与其他十字花科物种不同，经受强光照的*H. incana*可通过三种独特机制提升光合作用相关基因的表达量：经典差异表达、单拷贝基因的固有高表达，以及通过同时表达多个基因拷贝实现的累积高表达。本研究为后续解析光合光利用效率提升机制、最终实现农作物高效光合作用的相关工作奠定了重要基础。