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Fig. 3 | Biotechnology for Biofuels

Fig. 3

From: Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation

Fig. 3

Overview of the transcriptome dataset analysis. a Distribution of absolute transcript abundances as FPKM values from all time points on a half-log scale (log10). In the box-whisker plot representation, the thick line represents the median value, the colored box represents the interval between the first and third quartiles, the two whiskers indicate the respective 1.5× interquartile ranges, and the black dots mark the outliers. b Distribution of relative transcript abundance changes normalized to the reference time point N_0, expressed as fold change (FC) on a half-log scale (log2); box-whisker plots are as in (a). The black vertical line highlights the zero line (no regulation), while the light gray box indicates the threshold range where absolute log2-FC < 1 indicating no response to −N or N resupply. The dashed blue line indicates the threshold above which a transcript was considered as transcriptionally highly regulated, and above which the log2-FC was restricted to 4 and appropriately highlighted by darker color in Figs. 4, 5, 6 and Additional file 1: Figure S10. c Expression profile of the MLDP gene (XLOC_008097). Different colors represent the three stages of nitrogen availability: early −N (e−N, orange), late −N (l−N, brown), and N resupply (r+N, green). The reference time point N_0 is shown in gray. The light gray box highlights the threshold range where the absolute log2-FC relative to N_0 was less than one. d Dendrogram of a hierarchical clustering of time points using the CummeRbund package [154] with default settings. The red dotted line indicates the applied threshold yielding the four clusters (blue frames). e Venn diagrams of shared genes between the three stages of N availability. The sets on the left consist of genes classified as up-regulated by mean FC during the e−N stage (orange), during the l−N stage (brown), and during the r+N stage (green). On the right, the same was done for down-regulated genes

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