Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
PLoS One. 2012;7(6):e39704. doi: 10.1371/journal.pone.0039704. Epub 2012 Jun 27.
Light 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.
RNA-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.
Transcriptome 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.
光是影响紫菜生长发育的重要因素，但关于蓝光介导的生理响应及其分子机制的报道有限。本研究应用高通量 RNA 测序（RNA-seq）技术分别对紫菜暴露于蓝光和黑暗条件下的转录组进行分析。设计基因表达比较分析旨在从分子水平上关联蓝光的影响和生理机制。
RNA-seq 分析得到 70497 个非冗余的 unigenes，平均长度为 538bp。鉴定出 28358 个（40.2%）具有编码区的功能转录本。通过 Swissprot、Nr、GO、KEGG 和 COG 数据库注释，有 25924 个 unigenes与已知基因序列高度相似（E 值<10(-5))，43 个 unigenes可能是蓝光受体。10440 个 unigenes被分类到 Gene Ontology，8476 个 unigenes参与 114 个已知通路。根据 RPKM 值，在蓝光和黑暗处理之间检测到 11660 个（16.5%）差异表达的 unigenes，包括 7808 个上调和 3852 个下调的 unigenes，表明紫菜在蓝光暴露过程中经历了广泛的转录组重新编排。鉴定出的蓝光特异性响应基因参与了生物钟、类黄酮生物合成、光修复和光形态建成等过程。
紫菜转录组谱分析为潜在基因鉴定和未来功能基因组学研究提供了线索。对蓝光下表达变化的全面研究将增强我们对低等植物中蓝光诱导响应的分子机制的理解，并有助于未来蓝光受体的鉴定和特定响应途径的分析。
