Fig 1.
The length distribution of the de novo assembly for contigs (A) and unigenes (B).
The horizontal coordinates are contig lengths (A) or unigenes lengths (B), and the vertical coordinates are numbers of contigs (A) or unigenes (B). The length distribution of contigs and unigenes were counted from 200 nt to 3000 nt with an interval of 100 nt. Each number in the x-axis indicates a region of sequence length covering 100 nt, for example, ‘‘200” represents a region of sequence length between 200 to 300.
Table 1.
Summary of transcriptome sequencing.
Table 2.
Statistics of unigenes annotation using public databases.
Fig 2.
GO functions are listed in the X-axis. The Y-axis represents the number (right) and percentage (left) of genes that have the GO function.
Fig 3.
COG function classification of unigenes.
Table 3.
The top 10 KEGG pathway classifications of the transcriptome.
The small brackets denote the percentage of annotated unigenes in a pathway to the total number of unigenes.
Table 4.
Summary of reads mapped to reference genes of the de novo assembly of transcriptome.
NH, Normal nitrogen level and high temperature treatment; NN, Normal nitrogen level and normal temperature treatment; HH, High nitrogen level and high temperature treatment; HN, High nitrogen level and normal temperature treatment. Sample IDs were labeled as follows: “G” for the strain of rice used (Ganxin 203), four treatment combinations and a number for the two pooling duplicates.
Fig 4.
Chart listing statistics of the groups of differentially expressed genes.
The differentially expressed genes were identified with the criteria (twofold or more change and P< 0.001).
Fig 5.
Cluster image of differentially expressed genes levels.
Each column represents an experimental condition, and each row represents a gene that is differentially expressed. The log2 (RPKM) of differentially expressed genes were clustered, and red indicates upregulation and green indicates downregulation. Genes labeled with color closer to red than green, indicates a more highly expressed gene.
Table 5.
Summary of differentially expressed genes that occurred simultaneously in different samples.
All genes in this table were annotated by KEGG, GO, and BLAST NR databases, and showed differential expression with probability greater than or equal to 0.8 and |log2Ratio| greater than or equal to 1. Unigenes with positive log2Ratio represent upregulated, and genes with negative log2Ratio represent downregulated genes.
Fig 6.
KEGG pathway classification of differentially expressed genes.
RichFactor is the ratio of DEG numbers annotated in a given pathway term to all gene numbers that were annotated in the pathway term. Greater RichFactor means greater intensiveness. Q-value is the corrected P-value ranging from 0~1, and lower Q-value indicates greater intensiveness. The top 20 pathway terms enriched by the KEGG database are listed in this figure.
Fig 7.
Expression pattern of the selected genes by RT-qPCR and RNA-seq analysis.
(A) Gene expression data for RNA-seq analysis. (B) The RT-qPCR analysis of gene expression data. The fold changes of the genes are shown on the y-axis.
Fig 8.
Effects of nitrogen level and high temperature at late spikelet differentiation stage on spikelet fertility of rice.
Bargraph data show as mean ± standard error. Bars marked with the same letters indicate no significant difference at 5% level or 1% level. NH, Normal nitrogen level with high temperature; NN, Normal nitrogen level with normal temperature; HH, High nitrogen level with high temperature; HN, High nitrogen level with normal temperature.