title: Transcriptomic and physiological analysis of common duckweed Lemna minor responses to NH4(+) toxicity.
abstract: BACKGROUND
  Plants can suffer ammonium (NH4 (+)) toxicity, particularly when NH4 (+) is supplied as the sole nitrogen source. However, our knowledge about the underlying mechanisms of NH4 (+) toxicity is still largely unknown. Lemna minor, a model duckweed species, can grow well in high NH4 (+) environment but to some extent can also suffer toxic effects. The transcriptomic and physiological analysis of L. minor responding to high NH4 (+) may provide us some interesting and useful information not only in toxic processes, but also in tolerance mechanisms.
  
  
  RESULTS
  The L. minor cultured in the Hoagland solution were used as the control (NC), and in two NH4 (+) concentrations (NH4 (+) was the sole nitrogen source), 84 mg/L (A84) and 840 mg/L (A840) were used as stress treatments. The NH4 (+) toxicity could inhibit the growth of L. minor. Reactive oxygen species (ROS) and cell death were studied using stained fronds under toxic levels of NH4 (+). The malondialdehyde content and the activities of superoxide dismutase and peroxidase increased from NC to A840, rather than catalase and ascorbate peroxidase. A total of 6.62G nucleotides were generated from the three distinct libraries. A total of 14,207 differentially expressed genes (DEGs) among 70,728 unigenes were obtained. All the DEGs could be clustered into 7 profiles. Most DEGs were down-regulated under NH4 (+) toxicity. The genes required for lignin biosynthesis in phenylpropanoid biosynthesis pathway were up-regulated. ROS oxidative-related genes and programmed cell death (PCD)-related genes were also analyzed and indicated oxidative damage and PCD occurring under NH4 (+) toxicity.
  
  
  CONCLUSIONS
  The first large transcriptome study in L. minor responses to NH4 (+) toxicity was reported in this work. NH4 (+) toxicity could induce ROS accumulation that causes oxidative damage and thus induce cell death in L. minor. The antioxidant enzyme system was activated under NH4 (+) toxicity for ROS scavenging. The phenylpropanoid pathway was stimulated under NH4 (+) toxicity. The increased lignin biosynthesis might play an important role in NH4 (+) toxicity resistance.
authors.affiliation: Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041, Sichuan, PR China. wangwenguo@caas.cn.|Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041, Sichuan, PR China. wangwenguo@caas.cn.
authors.forename: Wenguo
authors.initials: W
authors.lastname: Wang
authors.affiliation: Faculty of Biotechnology Industry, Chengdu University, 1 Shiling Street, Chengluo Road, 610106, Chengdu, Sichuan, PR China.
authors.forename: Rui
authors.initials: R
authors.lastname: Li
authors.affiliation: Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041, Sichuan, PR China.|Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041, Sichuan, PR China.
authors.forename: Qili
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041, Sichuan, PR China.|Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041, Sichuan, PR China.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Tang
authors.affiliation: Faculty of Biotechnology Industry, Chengdu University, 1 Shiling Street, Chengluo Road, 610106, Chengdu, Sichuan, PR China. zhaoqi@cdu.edu.cn.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhao
mesh_terms: D064751:Ammonium Compounds / Q000633:toxicity*; D029064:Araceae / Q000187:drug effects* / Q000235:genetics / Q000502:physiology; D053898:Biosynthetic Pathways / Q000235:genetics; D004305:Dose-Response Relationship, Drug; D004789:Enzyme Activation / Q000187:drug effects; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D015723:Gene Library; D063990:Gene Ontology; D018527:Hydroponics / Q000379:methods; D008031:Lignin / Q000096:biosynthesis; D008315:Malondialdehyde / Q000378:metabolism; D009195:Peroxidase / Q000378:metabolism; D017382:Reactive Oxygen Species / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods; D013482:Superoxide Dismutase / Q000378:metabolism
chemical_list: D064751:Ammonium Compounds; D017382:Reactive Oxygen Species; D008315:Malondialdehyde; D008031:Lignin; D009195:Peroxidase; D013482:Superoxide Dismutase
keywords: Lemna minor; Lignin biosynthesis; NH4 + toxicity; Oxidative damage; Phenylpropanoid pathway; Programmed cell death; RNA-seq; Transcriptome