Transcriptome Sequencing and Comparative Analysis of Saccharina japonica (Laminariales, Phaeophyceae) under Blue Light Induction

Abstract

BackgroundLight has significant effect on the growth and development of Saccharina japonica, but there are limited reports on blue light mediated physiological responses and molecular mechanism. In this study, high-throughput paired-end RNA-sequencing (RNA-Seq) technology was applied to transcriptomes of S. japonica exposed to blue light and darkness, respectively. Comparative analysis of gene expression was designed to correlate the effect of blue light and physiological mechanisms on the molecular level.Principal FindingsRNA-seq analysis yielded 70,497 non-redundant unigenes with an average length of 538 bp. 28,358 (40.2%) functional transcripts encoding regions were identified. Annotation through Swissprot, Nr, GO, KEGG, and COG databases showed 25,924 unigenes compared well (E-value <10−5) with known gene sequences, and 43 unigenes were putative BL photoreceptor. 10,440 unigenes were classified into Gene Ontology, and 8,476 unigenes were involved in 114 known pathways. Based on RPKM values, 11,660 (16.5%) differentially expressed unigenes were detected between blue light and dark exposed treatments, including 7,808 upregulated and 3,852 downregulated unigenes, suggesting S. japonica had undergone extensive transcriptome re-orchestration during BL exposure. The BL-specific responsive genes were indentified to function in processes of circadian rhythm, flavonoid biosynthesis, photoreactivation and photomorphogenesis.SignificanceTranscriptome profiling of S. japonica provides clues to potential genes identification and future functional genomics study. The global survey of expression changes under blue light will enhance our understanding of molecular mechanisms underlying blue light induced responses in lower plants as well as facilitate future blue light photoreceptor identification and specific responsive pathways analysis.

Seaweed reproductive biology: environmental and genetic controls

“…Instead of phytochrome, stramenopiles possess their own blue light photoreceptor, aureochrome (Takahashi et al 2007). The transcriptome of Saccharina japonica sporophytes under blue light was characterized by Deng et al (2012), while differential gene expression under blue and red light was studied by Wang et al (2013). The results indicated that the number of differentially expressed genes was significantly higher under red light conditions compared to blue light.…”

De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)

“…Alternatively, the transcriptome analysis based on the next generation sequencing (NGS) is more attractive in identifying the expression gene for its characteristics of cost-efficient, high throughput and rapidness. NGS, including the Roche/454 Genome Sequencer FLX Instrument, the ABI SOLiD System and the Illumina Genome Analyser, was a powerful tool and was untilized in many researching areas, including re-sequencing, micro-RNA expression profiling, DNA methylation, especially de novo transcriptome sequencing for non-model organisms [5-13]. Recently, based on the NGS technology, the transcriptome of many species such as chestnut [9], coral larval [5], sweetpotato [11], ginseng root [10], chickpea [12] and saccharina japonica [13] had been analyzed, which has accelerated our understanding of the complexity of expression, regulation and networks of gene in model and non-model organisms.…”

Transcriptome Sequencing and Comparative Analysis of Piptoporus betulinus in Response to Birch Sawdust Induction

“…The fragments per kilo bases per million reads (FPKM) were used to evaluate expressed values and quantify transcript levels, which normalizes and eliminates the influence of gene length and sequencing depth in calculating gene expression, allowing for direct comparison of gene expression between different treatments [20]. Genes with an adjusted p-value < 0.05 was assigned as differentially expressed according to the reports of Deng et al [21]. For pathway enrichment analysis, all differentially expressed unigenes were submitted in the online KEGG Automatic Annotation Server (http://www.…”