State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, PR China.
Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, PR China.
Ecotoxicol Environ Saf. 2021 Feb;209:111816. doi: 10.1016/j.ecoenv.2020.111816. Epub 2020 Dec 21.
As a non-essential heavy metal, cadmium (Cd) is toxic to plants. In the last 15 years, over 70 transcriptome studies have been published to decipher the molecular response mechanism against Cd stress in different plants. To extract generalization results from transcriptomic data across different plants and obtain some hub genes that respond to Cd stress, we carried out a meta-analysis of 32 published datasets. Cluster analysis revealed that plant species played a more decisive role than the media used and exposure time in the transcriptome patterns of plant roots response to Cd. The datasets from a Gramineae-like (GL) group were closer in clustering. 838 DEGs were commonly Cd-regulated in at least nine of 18 GL datasets. Gene ontology and KEGG pathway analyses revealed that oxidative stress-related terms and lignin synthesis-related terms were significantly enriched. Mapman analysis revealed that these common DEGs were mainly involved in regulation, cellular response, secondary metabolism, transport, cell wall and lipid metabolism. In Oryza sativa, 15 DEGs were up-regulated in at least four of five HM (As, Cr, Cd, Hg and Pb) groups, such as Os10g0517500 (methionine gamma-lyase) and Os01g0159800 (bHLH107). Moreover, our datasets can be used to retrieve log2FC value of specific genes across 29 studies (48 datasets), which provides data reference for the subsequent selection of HM-related genes. Our results provide the basis for further understanding of Cd tolerance mechanisms in plants.
作为一种非必需的重金属，镉（Cd）对植物有毒。在过去的 15 年中，已有超过 70 项转录组研究发表，以破译不同植物应对 Cd 胁迫的分子响应机制。为了从不同植物的转录组数据中提取概括结果，并获得一些对 Cd 胁迫有响应的枢纽基因，我们对 32 个已发表的数据集进行了荟萃分析。聚类分析表明，植物物种比所用的培养基和暴露时间对植物根系对 Cd 响应的转录组模式起着更决定性的作用。来自禾本科（GL）类群的数据集在聚类中更为接近。在至少 18 个 GL 数据集中的 9 个数据集中共发现了 838 个 Cd 调控的差异表达基因（DEGs）。GO 和 KEGG 通路分析表明，与氧化应激相关的术语和木质素合成相关的术语显著富集。Mapman 分析表明，这些共同的 DEGs 主要参与调控、细胞反应、次生代谢、运输、细胞壁和脂质代谢。在水稻中，在至少 5 个重金属（As、Cr、Cd、Hg 和 Pb）组中的 4 个或更多组中，有 15 个 DEGs 上调，如 Os10g0517500（蛋氨酸γ-裂解酶）和 Os01g0159800（bHLH107）。此外，我们的数据集可用于检索 29 项研究（48 个数据集）中特定基因的 log2FC 值，为随后选择重金属相关基因提供了数据参考。我们的研究结果为进一步理解植物对 Cd 的耐受机制提供了基础。
