Chan Cheong Xin, Blouin Nicolas A, Zhuang Yunyun, Zäuner Simone, Prochnik Simon E, Lindquist Erika, Lin Senjie, Benning Christoph, Lohr Martin, Yarish Charles, Gantt Elisabeth, Grossman Arthur R, Lu Shan, Müller Kirsten, W Stiller John, Brawley Susan H, Bhattacharya Debashish
Department of Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, 08901, USA.
School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA.
J Phycol. 2012 Dec;48(6):1328-42. doi: 10.1111/j.1529-8817.2012.01229.x. Epub 2012 Oct 3.
The red seaweed Porphyra (Bangiophyceae) and related Bangiales have global economic importance. Here, we report the analysis of a comprehensive transcriptome comprising ca. 4.7 million expressed sequence tag (EST) reads from P. umbilicalis (L.) J. Agardh and P. purpurea (Roth) C. Agardh (ca. 980 Mbp of data generated using 454 FLX pyrosequencing). These ESTs were isolated from the haploid gametophyte (blades from both species) and diploid conchocelis stage (from P. purpurea). In a bioinformatic analysis, only 20% of the contigs were found to encode proteins of known biological function. Comparative analysis of predicted protein functions in mesophilic (including Porphyra) and extremophilic red algae suggest that the former has more putative functions related to signaling, membrane transport processes, and establishment of protein complexes. These enhanced functions may reflect general mesophilic adaptations. A near-complete repertoire of genes encoding histones and ribosomal proteins was identified, with some differentially regulated between the blade and conchocelis stage in P. purpurea. This finding may reflect specific regulatory processes associated with these distinct phases of the life history. Fatty acid desaturation patterns, in combination with gene expression profiles, demonstrate differences from seed plants with respect to the transport of fatty acid/lipid among subcellular compartments and the molecular machinery of lipid assembly. We also recovered a near-complete gene repertoire for enzymes involved in the formation of sterols and carotenoids, including candidate genes for the biosynthesis of lutein. Our findings provide key insights into the evolution, development, and biology of Porphyra, an important lineage of red algae.
红藻紫菜属（红毛菜纲）及相关的红毛菜目具有全球经济重要性。在此，我们报告了对一个综合转录组的分析，该转录组包含约470万个来自脐形紫菜（L.）J. 阿加德和紫球紫菜（Roth）C. 阿加德的表达序列标签（EST）读数（使用454 FLX焦磷酸测序产生约980兆碱基对的数据）。这些EST是从单倍体配子体（两个物种的叶片）和二倍体壳孢子体阶段（来自紫球紫菜）分离得到的。在生物信息学分析中，仅发现20%的重叠群编码具有已知生物学功能的蛋白质。对嗜温红藻（包括紫菜属）和嗜极红藻中预测蛋白质功能的比较分析表明，前者具有更多与信号传导、膜运输过程和蛋白质复合物形成相关的推定功能。这些增强的功能可能反映了一般的嗜温适应性。鉴定出了一个几乎完整的编码组蛋白和核糖体蛋白的基因库，紫球紫菜的叶片和壳孢子体阶段之间存在一些差异调节。这一发现可能反映了与生活史这些不同阶段相关的特定调节过程。脂肪酸去饱和模式与基因表达谱相结合，表明在脂肪酸/脂质在亚细胞区室之间的运输以及脂质组装的分子机制方面与种子植物存在差异。我们还获得了一个几乎完整的参与甾醇和类胡萝卜素形成的酶的基因库，包括叶黄素生物合成的候选基因。我们的研究结果为红藻的重要谱系紫菜属的进化、发育和生物学提供了关键见解。
