| As an ecological phenomenon, harmful algal blooms (HABs) or’red tides’has obtained wide attention, for its serious impact on the human health, environment, aquaculture, fisheries and tourism. The outbreak of’red tides’have been studied in the field of ecology and physiology. However, the research is limited in the field of molecular mechanism. Skeletonema marinoi is an important diatom of HABs. However, the study on S. marinoi mainly focused on the biochemistry, physiological ecology, metabolomics and marine geography, and the molecular background information is scant, reflecting a lack of basic genomic and transcriptomic data.Using Illumna high-throughout sequencing technology, the transcriptome and expression profiles of S. marinoi were sequenced and analyzed. Comprehensive and systematic study of transcriptomic characteristics, analysis of characteristics of Digital Gene Expression Profiling during different growth phase and deep exploration of molecular mechanism for response to the temperature and low silicate stress environment will provide a comprehensive insight into gene expression profiles and provides an important gene resource for future genetic and molecular studies of S. marinoi and other Skeletonema family diatom.The major content and the results are as follows:The global transcriptome of S. marinoi was sequenced using Illumina high-throughput sequencing technology. A total of 117,184,612,117 clean reads (11.7Gb clean bases) were generated from the cDNA library constructed for a RNA mixture of S. marinoi at different development stages and under different stress treatments. These clean reads were assembled into 20,319 unigenes with a mean length of 1,602 bp. A total of 171,260 predicted SNPs,9464 InDels and 3220 SSRs were identified from 20,319 assembled unigenes. Based on sequence similarity searches with known proteins, a large number of genes related to stress response were found, including genes related to temperature stress, antioxidant system, light stress, nutrients stress and other genes related to stress processes. And Many genes related to developmental process, cell cycle, apoptosis, phagosome, MAPK signaling pathway, calcium signaling pathway, plant hormone signal transduction, ubiquitin mediated proteolysis, Glycolysis/Gluconeogenesis, pyruvate metabolism, biosynthesis of unsaturated fatty acids, fatty acid biosynthesis and fatty acid metabolism were also found in S. marinoi.In order to study the expression profile characteristics during different growth phases, the cDNA library was constructed for nine samples from the different growth phases and then sequenced by Illumina sequencing technology (three biological replicates for each treatment). A total of 7.74M-12.86M clean reads were obtained for each sample. Moreover, the number of reads mapped to transcriptome is 92.16%-94.55% of the total reads number. By analysis of the overall pattern of gene expression during declining phase (compared with the exponential phase), a total of 2706 differentially expressed genes were identified. Comparisons of gene expression showed that 2,706 genes were differentially expressed between DP and EP (DP vs EP),1,544 genes were differentially expressed between SP and EP (SP vs EP),95 genes were differentially expressed between SP and DP (SP vs DP) (padj<0.05). According to the expression pattern for DP vs EP,2,706 unigenes were differentially expressed, including 1,096 obviously up-regulated genes in DP and 1610 genes that were obviously down-regulated. GO and KEGG enrichment analysis showed that a number of different expression unigenes related to energy metabolism, cell cycle, apoptosis, fatty acid biosynthesis and fatty acid metabolism, cytoskeleton and microtubule-based movement during different growth phases. Moreover, we found that the cytoskeleton related genes were constantly down-regulated from exponential phase to declining phase.In order to study the expression profile characteristics in response to temperature stress environment in S. marinoi, the cDNA library was constructed for samples from the different temperature stress treatments and then sequenced by Illumina sequencing technology. A total of 10.60M-14.46M clean reads were obtained for each sample. Moreover, the number of reads mapped to transcriptome is 92.16%-93.84% of the total reads number. There were 1178 genes identified as significant differentially expressed between low temperature stress and control group, among them 659 were up-regulated and 519 down-regulated in low temperature stress. There were 247 genes identified as significant differentially expressed between high temperature stress and control group, among them 128 were up-regulated and 119 down-regulated in high temperature stress. Using software to classify the different expression genes with GO functions were mainly involved in structural constituent of ribosome, cellular macromolecule biosynthetic process, structural molecule activity, cellular component biogenesis, ribonucleoprotein complex biogenesis, Photosynthesis, carbon utilization, chlorophyll metabolic process between low temperature stress and control sample, and the KEGG functions classify were mainly involved in ribosome, fatty acid biosynthesis, porphyrin and chlorophyll metabolism, fatty acid metabolism, biotin metabolism, amino sugar and nucleotide sugar metabolism. GO and KEGG enrichment analysis showed that a number of different expression unigenes related to structural constituent of cell wall, plant-type cell wall organization, plant-type cell wall organization or biogenesis, unfolded protein binding, cell wall biogenesis, aminoacyl-tRNA biosynthesis, apoptosis, protein processing in endoplasmic reticulum, MAPK signaling pathway were significant enrichment between high temperature stress and control sample.In order to study the expression profile characteristics in response to low silicate stress environment in S. marinoi, the cDNA library was constructed for samples from the low silicate stress treatments and then sequenced by Illumina sequencing technology. A total of 9.60M-12.14M clean reads were obtained for each sample. Moreover, the number of reads mapped to transcriptome is 92.16%-93.69% of the total reads number. There were 258 genes identified as significant differentially expressed between low silicate stress and control group, among them 62 were up-regulated and 196 down-regulated in low silicate stress. In the low silicate stress sample, GO enrichment analysis show that the different expression genes mainly involved in microtubule, photosynthesis, light harvesting, silicate transport, and the KEGG functions classify were mainly involved in pyruvate metabolism, glycolysis/gluconeogenesis. |
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