Comparative transcriptome analysis reveals heat stress-responsive genes and their signalling pathways in lilies (Lilium longiflorum vs. Lilium distichum)

Yongyao Fu,Hongqun Li,Qiang Li,Liping Yang,Jian Gao,Xu Wenji,Haihong Gao,Xiang Jia Min

doi:10.1371/journal.pone.0239605

Abstract

The lily, a famous bulbous flower, is seriously affected by high temperatures, which affect their growth and production. To date, the signalling pathways and the molecular mechanisms related to heat response in Lilium have not been elucidated. In this study, a comparative transcriptome analysis was performed in an important thermo-tolerant flower, L. longiflorum, and a thermo-sensitive flower, L. distichum. Lily seedlings were first exposed to heat stress at 42°C for different lengths of time, and the optimal time-points (2 h and 24 h) were selected for RNA sequencing (RNA-seq). Approximately 66.51, 66.21, and 65.36 Mb clean reads were identified from three libraries of L. longiflorum (LL_CK, LL_T2h and LL_T24h, respectively) and 66.18, 66.03, and 65.16 Mb clean reads were obtained from three libraries of L. distichum (LD_CK, LD_T2h and LD_T24h, respectively) after rRNA removing. A total of 34,301 unigenes showed similarity to known proteins in the database NCBI non-redundant protein (NR), Swiss-Prot proteins, InterPro proteins, Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG). In addition, 1,621 genes were differentially expressed in the overlapping libraries between LL_DEGs and LD_DEGs; of these genes, 352 DEGs were obviously upregulated in L. longiflorum and downregulated in L. distichum during heat stress, including 4-coumarate, CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (CCoAOMT), peroxidase, pathogenesis-related protein 10 family genes (PR10s), 14-3-3 protein, leucine-rich repeat receptor-like protein kinase, and glycine-rich cell wall structural protein-like. These genes were mainly involved in metabolic pathways, phenylpropanoid biosynthesis, plant-pathogen interactions, plant hormone signal transduction, and kinase signalling pathways. Quantitative RT-PCR was performed to validate the expression profiling of these DEGs in RNA-seq data. Taken together, the results obtained in the present study provide a comprehensive sequence resource for the discovery of heat-resistance genes and reveal potential key components that are responsive to heat stress in lilies, which may help to elucidate the heat signal transcription networks and facilitate heat-resistance breeding in lily.

Highlights

High temperature is a significant environmental factor that affects plant growth and development
Transcription profiling of thermo tolerant and/or thermo susceptible genotypes has shown that many genes are influenced by high temperatures, including heat stress transcription factors (HSFs), heat shock proteins (HSPs), calmodulin CaM3 and genes involved in membrane fluidity, chromatin changes, RNA unfolding, enzymatic reactions, such as reactive oxygen species (ROS), and programmed cell death [7]
Physiological changes of lily seedings under heat stress conditions To determine the optimal time to analyse the heat response for lilies (L. longiflorum and L. distichum), uniform plantlets with 2 months of growth in aseptic conditions were subjected to high temperature (42 ̊C) treatment and sampled at six different times of stress (2 h, 8 h, 16 h, 24 h, 48 h and 72 h)

Summary

Introduction

High temperature is a significant environmental factor that affects plant growth and development. Transcription profiling of thermo tolerant and/or thermo susceptible genotypes has shown that many genes are influenced by high temperatures, including heat stress transcription factors (HSFs), heat shock proteins (HSPs), calmodulin CaM3 and genes involved in membrane fluidity, chromatin changes, RNA unfolding, enzymatic reactions, such as reactive oxygen species (ROS), and programmed cell death [7]. The upregulation of several genes has been reported to enhance plant tolerance to high temperatures These genes include Calmodulin-binding protein phosphatase PP7 [8], protein phosphatase RCF2 and NAC19 [9], HEAT-INDUCED TAS1 TARGET1 (HTT1) in Arabidopsis [10] and SUMO E3 Ligase SlSIZ1 in tomato [11], in addition to the numbers of HSFs that act as key transcription switches in regulating the activation of genes responsive to heat stress in virous plants [12]

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Conclusion