PDF(Pubmed)
Abstract：
Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.
摘要：
海洋微生物群落是海洋生态系统运作和生物多样性保护的基础。随着宏基因组学和超转录组学在海洋环境研究中的应用，在分析整个微生物群落的功能方面取得了重大进展。这些分子技术高度依赖于可靠的，有很好的特点,微生物的全面和分类多样的测序参考转录组。在这里，我们介绍了一组12个单独的转录组组件，这些组件来自亚得里亚海北部的6种代表性硅藻物种，这些硅藻物种在2种环境相关的生长条件下生长（磷酸盐充足与磷酸盐剥夺)。过滤读取和程序集后，每个组装平均获得64,932个转录本，其中平均8856个被分配给功能已知的蛋白质。在所有分配的成绩单中，平均有6483种蛋白质被分类为硅藻（Bacillariophyta）。平均而言,在大量培养基条件下生长的硅藻的转录组组装体中检测到较高数量的指定蛋白质。平均而言,两种生长条件之间共有50％的映射蛋白质。数据集中所有记录的蛋白质被分为24个COG类别，大约25%属于未知函数，其余75%属于所有其他类别。由此产生的北亚得里亚海硅藻参考数据库，重点关注作为该地区特征和对未来世界海洋预测的养分限制的响应，为分析环境转移组和宏基因组数据提供了宝贵的资源。每个北亚得里亚海转录组本身也可以用作将来将产生的相关物种的（元）转录组和基因表达研究的参考数据库。
