Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum - PubMed (original) (raw)

Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum

Jingjing Jin et al. BMC Genomics. 2017.

Abstract

Background: CB-1 and K326 are closely related tobacco cultivars; however, their cold tolerance capacities are different. K326 is much more cold tolerant than CB-1.

Results: We studied the transcriptomes and metabolomes of CB-1 and K326 leaf samples treated with cold stress. Totally, we have identified 14,590 differentially expressed genes (DEGs) in CB-1 and 14,605 DEGs in K326; there was also 200 differentially expressed metabolites in CB-1 and 194 in K326. Moreover, there were many overlapping genes (around 50%) that were cold-responsive in both plant cultivars, although there were also many differences in the cold responsive genes between the two cultivars. Importantly, for most of the overlapping cold responsive genes, the extent of the changes in expression were typically much more pronounced in K326 than in CB-1, which may help explain the superior cold tolerance of K326. Similar results were found in the metabolome analysis, particularly with the analysis of primary metabolites, including amino acids, organic acids, and sugars. The large number of specific responsive genes and metabolites highlight the complex regulatory mechanisms associated with cold stress in tobacco. In addition, our work implies that the energy metabolism and hormones may function distinctly between CB-1 and K326.

Conclusions: Differences in gene expression and metabolite levels following cold stress treatment seem likely to have contributed to the observed difference in the cold tolerance phenotype of these two tobacco cultivars.

Keywords: Cold stress; Metabolome; Tobacco; Transcriptome.

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Figures

Fig. 1

Fig. 1

Overview of transcriptome analysis. a Phenotype for K326 and CB-1 under cold treatment. Left Panel: untreated plants; Right Panel: Plants after cold treatment. Up Panel: Wildtype and cold treated K326 plants; Down Panel: Wildtype and cold treated CB-1 plants. b Venn graph for CB-1 and K326 based on cold up-regulated (induced) genes. c Venn graph for CB-1 and K326 based on cold down-regulated (repressed) genes. d Heatmap of DEG expression in CC, CT, KC, and KT

Fig. 2

Fig. 2

qRT-PCR analyses of unigenes. c44821_g1: MYB; c64865_g1: CRF6; c78380_g1: WRKY33; c79563_g1: DREB1D; c79891_g2: ERF109; c59823_g2: unknown; c63831_g1: ELF4; c64765_g1: DREB1F; c67085_g1: ARR6; c70415_g4: NFYB7; c70702_g2: DREB1B; c70842_g1: COR413; c71056_g1: DREB2H; c71107_g1: BHLH92; c72839_g1: ARR4; c73886_g1: DREB2A; c74180_g1: GAI; c74525_g2: ABR1; c75413_g1: RAV1; c77215_g2: unknown; c81375_g1: ERF053; c81815_g3: ARR14; c85046_g1: CMTA3; c85178_g2: AHK3; c85784_g1: HOS1; c85969_g1: AHK4; c86033_g1: ARR1; c86950_g3: SIZ1. ** means _p_-value < 0.01 between treatment and control; * means _p_-value < 0.05 between treatment and control

Fig. 3

Fig. 3

Top 30 enriched pathways for overlapping cold responsive genes between K326 and CB-1

Fig. 4

Fig. 4

Top 30 enriched pathways for specific cold responsive genes of CB-1 and K326. a Top 30 enriched pathways for CB-1 specific cold responsive genes. b Top 30 enriched pathways for K326 specific cold responsive genes

Fig. 5

Fig. 5

Classification of identified metabolites. a Venn graph for up-regulated differentially accumulated metabolites between CB-1 and K326. b Venn graph for down-regulated differentially accumulated metabolites between CB-1 and K326. c Pie graph for differentially accumulated metabolites in CB-1. d Pie graph for differentially accumulated metabolites in K326

Fig. 6

Fig. 6

Different patterns for CB-1 and K326 based on the identified secondary metabolites. a Boxplot for ethylene levels in CC, CT, KC, and KT. b Boxplot for salicylic acid levels in CC, CT, KC, and KT. c Heatmap of differentially accumulated secondary metabolites for CC, CT, KC, and KT

Fig. 7

Fig. 7

A parallel principal component analysis (PCA) of gene and metabolite profiles under cold treatment. Each point represents one experiments for gene expression and metabolite profiling. a PCA model for gene expression experiments. b PCA model for primary metabolite profiling. c PCA model for secondary metabolite profiling

Fig. 8

Fig. 8

The energy metabolism through sugar and amino acids metabolic pathways under cold treatment. Red color represents the fold change between wild type and cold stress in CB-1. Blue color represents the fold change between wild type and cold stress in K326

Fig. 9

Fig. 9

The levels of sugar metabolites and fatty acid metabolites. Y-axis represents the relative quantitate level of metabolites. a The relative metabolite levels for sugars. b The relative metabolite levels for fatty acids

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