Fig 1.
Analysis of Diameter at Breast Height (DBH) growth of poplar under different planting densities.
Nine-year-old poplar trees were grown under high (HD) and low (LD) planting density and their DBH was measured.** indicates significant difference at a level of 0.01 by one-way ANOVA using a Duncan t test.
Fig 2.
Heatmap showing gene expression at three vertical positions on poplar trees under different planting densities.
Gene expression was analyzed at three positions on poplar trees, upper (U), middle (M) and bottom (B), that were grown under two planting densities, high (HD) and low (LD). Blue indicates low expression levels and red indicates high expression levels.
Fig 3.
Gene expression profiles of differentially expressed genes (DEGs) in all comparison groups.
Samples were taken from poplar trees at three vertical positions: upper (U), middle (M) and bottom (B). The trees were grown under high (HD) and low planting density (LD). (A) The number of DEGs between HD and LD for three different comparisons (one for each vertical position). The red bars represent the number of upregulated DEGs under HD, while the green bars represent the number of DEGs downregulated under HD. The vertical ordinate represents the number of DEGs. (B) Distribution of the DEGs identified when HD is compared to LD that are common and specific to the upper, middle, and bottom positions.
Fig 4.
Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) unique to each vertical position.
DEGs were identified by comparing samples from poplar trees planted under high (HD) and low (LD) density. The samples were taken from three vertical positions for the comparisons: upper (U), middle (M), and bottom (B). The top 20 most enriched GO terms of the DEGs unique to each vertical position are shown: upper (A), middle (B) and bottom (C). Yellow bars represent “biological process,” green represent “cellular component,” and red represent “molecular function” GO categories. All terms had a false discovery rate (FDR) <0.05, except for “cellular component” terms in the middle and bottom density comparisons (FDR <0.1).
Fig 5.
The top 10 KEGG enrichments for differentially expressed genes (DEGs) found when comparing planting densities.
DEGs were identified by comparing samples from poplar trees planted under high (HD) and low (LD) density. The samples were taken from three vertical positions for the comparisons: upper (U), middle (M), and bottom (B). The top 10 most enriched KEGG pathways of the DEGs unique to each vertical position are shown. The bars colored green, blue, and red indicate the KEGG pathways with different enrichment levels (q <0.05, p <0.05 but q >0.05, p <0.1, respectively).
Fig 6.
Heat map of the expression levels of the 37 planting density-regulated differentially expressed genes (DEGs).
DEGs were identified by comparing samples from poplar trees planted under high (HD) and low (LD) density. The samples were taken from three vertical positions for comparisons: upper (U), middle (M), and bottom (B).
Fig 7.
Expression of DEGs involved in response to light and photosynthesis.
Differentially expressed genes (DEGs) were identified by comparing samples from poplar trees planted under high (HD) and low (LD) density. The samples were taken from three vertical positions for the comparisons: upper (U), middle (M), and bottom (B). (A) A heat map of the expression levels of DEGs that were found to be involved in response to light stimuli. (B) A heat map of the expression levels of DEGs involved in photosynthesis. (C) The structure of photosynthesis-antenna proteins. (D) The structure and mechanism of photosynthesis.
Fig 8.
DEGs related to the auxin/indole-3-acetic acid (AUX/IAA) signal transduction pathway.
Differentially expressed genes (DEGs) were identified by comparing samples from poplar trees planted under high (HD) and low (LD) density. The samples were taken from three vertical positions for the comparisons: upper (U), middle (M), and bottom (B). (A) A heat map of expression levels of the DEGs related to AUX/IAA. (B) The DEGs involved in the AUX/IAA signal transduction pathway.
Fig 9.
Expression of DEGs involved in carbon and nitrogen metabolism.
Differentially expressed genes (DEGs) were identified by comparing samples from poplar trees planted under high (HD) and low (LD) density. The samples were taken from three vertical positions for the comparisons: upper (U), middle (M), and bottom (B).
Fig 10.
The role of identified DEGs in carbon and nitrogen metabolism pathways.
(A) DEGs involved in the “carbon metabolism” pathway. (B) DEGs involved in the “carbon fixation in photosynthetic organisms” pathway. (C) DEGs involved in the “nitrogen metabolism” pathway.
Fig 11.
Comparison of expression patterns of 10 randomly selected genes based on the results of RNA-seq and qRT-PCR.
The x-axis represents the 10 randomly selected genes and the y-axis represents the value of log2 (relative expression). The blue histogram represents results from RNA-Seq and the red line represents results from qRT-PCR. Error bars indicate the standard deviation of the qRT-PCR data.