Table SI - RNAseq from The genomes uncoupled-dependent signalling pathway coordinates plastid biogenesis with the synthesis of anthocyanins

In recent years, it became evident that plants perceive, integrate and communicate abiotic stress signals through chloroplasts. During the process of acclimation plastid-derived, retrograde signals control nuclear gene expression in response to developmental and environmental cues leading to complex genetic and metabolic reprogramming to preserve cellular homeostasis under challenging environmental conditions. Upon stress-induced dysfunction of chloroplasts, GENOMES UNCOUPLED (GUN) proteins participate in the repression of PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES. Here, we show that the retrograde signal emitted by, or communicated through, GUN-proteins is also essential to induce the accumulation of photoprotective anthocyanin pigments when chloroplast development is attenuated. Comparative whole transcriptome sequencing and genetic analysis reveal GUN1 and GUN5-dependent signals as a source for the regulation of genes involved in anthocyanin biosynthesis. The signal transduction cascade includes well-known transcription factors for the control of anthocyanin biosynthesis, which are deregulated in gun mutants. We propose that regulation of PHANGs and genes contributing to anthocyanin biosynthesis are two, albeit oppositely, co-regulated processes during plastid biogenesis.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.近年来的研究表明，植物可通过叶绿体感知、整合并传递非生物胁迫信号。在植物适应胁迫的过程中，质体来源的逆行信号（retrograde signal）会响应发育与环境信号调控核基因表达，进而引发复杂的遗传与代谢重编程，以在恶劣环境条件下维持细胞稳态。当胁迫引发叶绿体功能异常时，基因组解偶联（GENOMES UNCOUPLED，简称GUN）蛋白会参与抑制光合作用相关核基因（PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES，下文简称PHANGs）的表达。本研究发现，在叶绿体发育受阻时，由GUN蛋白介导或传递的逆行信号，对于诱导光保护型花青素的积累同样不可或缺。通过全转录组测序比对与遗传分析，本研究揭示依赖GUN1与GUN5的信号通路是调控花青素生物合成相关基因的关键来源。该信号转导级联反应包含调控花青素生物合成的经典转录因子，此类因子在gun突变体中存在表达失调现象。我们提出，在质体生物发生过程中，PHANGs的调控与花青素生物合成相关基因的调控是两个虽方向相反但协同调控的过程。本文属于“内共生细胞器的逆行信号”专题栏目的一部分。