Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom

Abstract

Background: Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even though intensive studies have been conducted so far, the molecular mechanism behind harmful algal bloom was not fully understood. There are two major diatoms have been sequenced, but more diatoms should be examined at the whole genome level, and evolutionary genome studies were required to understand the landscape of molecular mechanism of the harmful algal bloom.

Results: Here we sequenced the genome of Skeletonema costatum, which is the dominant diatom in Japan causing a harmful algal bloom, and also performed RNA-sequencing analysis for conditions where harmful algal blooms often occur. As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to cytokinin is a key for the proliferation of the diatom.

Conclusions: Diatoms causing harmful algal blooms have gained multi-copy of genes related to oxidative stress response and response to cytokinin and obtained an ability to intensive gene expression at the blooms.

Keywords: Genome; Harmful algal bloom; Oxidative stress response; Red tide; Response to cytokinin; Transcriptome.

Fig. 1

Genome size estimation by k-mer analysis and the common eukaryotic genes conservation rate. K-mer analysis represents best k-mer as 25-mer and the estimated genome size is 51,364,529 bp (a). BUSCO analysis represents conservation rate of the common eukaryotic genes for four different assemblies. Color key is described in the figure (b)

Fig. 2

Orthologous analysis and Gene set enrichment analysis of common genes of harmful algal bloom, Sc-specific genes, and Sc-duplicated genes. a Venn diagram of sharing pattern of orthologous gene groups. The digit indicates the number of orthologous gene groups. Sc singlet genes represents the number of non-orthologous genes in Sc, and passed to the list of Sc-specific genes. b The number of genes in the orthologous gene groups. First column represents conservation pattern of orthologous genes in S-Sc, T-Tp, P-Pt, V-Vb. For example, STPV has 2798 orthologous group as shown in the panel A, and includes 4375 genes in Sc, 3699 genes in Pt. c Gene set enrichment analysis of the common genes for the harmful algal bloom. d Gene set enrichment analysis of Sc-specific genes. e Gene set enrichment analysis of Sc-duplicated genes

Fig. 3

Differentially expressed genes extracted from RNA-seq data under different conditions. a Differentially expressed genes among Sc culture samples for different temperatures, 10 °C, 18 °C, and 28 °C. 143 genes were extracted as highly expressed genes at high temperatures with FC > 2. These 143 genes were then used in the gene set enrichment analysis. As oxidative stress pathway was enriched, gene expression intensities of relative genes were extracted and used in the heatmap shown in the right-hand side. b Differentially expressed genes among Sc culture samples for different light conditions. 251 genes were extracted as highly expressed genes at lighter condition with FC > 2. Following steps are the same as above. c Differentially expressed genes among Sc culture samples for different nutrient conditions. 233 genes were extracted as highly expressed genes at abundant nitrogen condition. Following steps are the same as above

Fig. 4

Differentially expressed genes related to Oxidation reduction process and Response to cytokinin on the venn diagram. Grey rectangle represents the number of differentially expressed genes under different temperatures (up), different light conditions (middle), and different nutrient condition (bottom). Black rectangle represents the number of differentially expressed genes under different temperatures (up), different light conditions (middle), and different nutrient condition (bottom)

Fig. 5

Detailed analysis of gene expression differences under different conditions on oxidation reduction pathway (a) and the response to cytokinin process (b). Red to green color represents log gene expression of ROS, SOD, RBO, and other genes involved in the pathway (a), and LOG, IPT, UGT, CKX, ARR, AK, AHK, CYP735A1, CYP735A2, and other genes involved in the pathway (b). Pathways was modified from the figures in “The new insights into cadmium” (Jagna Chmielowska-Bąk et al.,2014), and “Antagonistic roles of abscisic acid and cytokinin” (Yandu Lu et al.,2014), respectively