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Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways - PubMed

  • ️Thu Jan 01 2015

Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways

Ying Zhao et al. Front Plant Sci. 2015.

Abstract

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Samples from hormone-treated cone reproductive shoots and naturally occurring non-cone setting shoots were analyzed using 24 digital gene expression (DGE) tag profiles using Illumina, generating a total of 69,520 putative transcripts. Next, 32 differentially and specifically expressed transcripts were determined using quantitative real-time polymerase chain reaction, including the upregulation of MADS-box transcription factors involved in male bud transition and flowering time control proteins involved in female bud transition. These differentially expressed transcripts were associated with 243 KEGG pathways. Among the significantly changed pathways, sugar pathways were mediated by hormone signals during the vegetative-to-reproductive phase transition, including glycolysis/gluconeogenesis and sucrose and starch metabolism pathways. Key enzymes were identified in these pathways, including alcohol dehydrogenase (NAD) and glutathione dehydrogenase for the glycolysis/gluconeogenesis pathway, and glucanphosphorylase for sucrose and starch metabolism pathways. Our results increase our understanding of the reproductive bud transition in gymnosperms. In addition, these studies on hormone-mediated sugar pathways increase our understanding of the relationship between sugar and hormone signaling during female and male bud initiation in Metasequoia.

Keywords: DGE; MADS-box; Metasequoia; hormone; male and female bud; sugar.

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Figures

Figure 1
Figure 1

Male buds and female cones on hormone-treated shoots. (A) Shoots before hormone treatment collected on May 24th, 2013. (B) Shoots before hormone treatment collected on June 11th, 2013. (C) Male buds on treated shoots collected on Sept 15th, 2013. (D) Male cones on treated shoots collected on Feb 5th, 2014. (E) Female buds on treated shoots collected on Oct16th, 2013. (F) Female buds on treated shoots collected on Mar 5th, 2014. (G) Untreated shoots (control) with vegetative buds collected on Oct 16th, 2013. (H) Untreated shoot (control) with vegetative buds collected on Mar 5th, 2014.

Figure 2
Figure 2

The size (bp) distribution of PUTs.

Figure 3
Figure 3

Differentially expressed genes in different comparisons.

Figure 4
Figure 4

Gene classification based on gene ontology (GO) for differentially expressed genes in Metasequoia in CK4 vs. TR4 comparison in biological processes. The frequency of GO terms was analyzed using GO slim assignment. The x-axis and y-axis indicate the names of clusters and the percentage of each cluster, respectively.

Figure 5
Figure 5

Venn diagrams with numbers of shared and unique differentially expressed genes. (A) DE genes between CK1 vs. TR1, CK2 vs. TR2, CK1 vs. CK2, and TR1 vs. TR2. (B) DE genes between CK3 vs. TR3, CK4 vs. TR4, CK3 vs. CK4, and TR3 vs. TR4.

Figure 6
Figure 6

Heat map showing the relative expression level for Metasequoia MADS-box genes in different stages during vegetative to reproductive phase transition based on DGE data analysis. The color scale (−1.5 to 1.5) represents the Z-score calculated by comparing Reads Per Kilobase of exon model per Million mapped reads (RPKM). Hierarchical clustering of genes and samples was shown in the dendrogram on the top and side of the heatmap using the complete linkage approach.

Figure 7
Figure 7

Multiple interactions among the genes involved in vegetative to reproductive phase transition and pathways of starch and sucrose metabolism and glycolysis/gluconeogenesis in response to hormone signaling. Colored rectangles correspond with the Matesequoia genes detected using DGE.

Figure 8
Figure 8

Correlation between qPCR and Illumina sequencing data. Correlation between qRT-PCR and Illumina sequencing data of 32 selected genes: 17 upregulated genes and 15 downregulated genes in 16 pairs of amplified RNA samples. Spearman Rank Correlation coefficient = 0.81 (P < 0.05).

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