CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Basic Medical Sciences, China Three Gorges University, Yichang 443000, China.
Sci Total Environ. 2023 Nov 1;897:165384. doi: 10.1016/j.scitotenv.2023.165384. Epub 2023 Jul 7.
Diatom species of the genus Skeletonema are dominant in global coastal waters with important roles in marine primary production and global biogeochemical cycling. Many Skeletonema species have been extensively studied also because they can cause harmful algae blooms (HABs) with negative impacts on marine ecosystems and aquaculture. In this study, the first chromosome-level assembly of the genome of Skeletonema marinoi was constructed. The genome size was 64.99 Mb with a contig N50 of 1.95 Mb. Up to 97.12 % of contigs were successfully anchored on 24 chromosomes. Analysis of the annotated genes revealed 28 large syntenic blocks with 2397 collinear gene pairs in the genome of S. marinoi, suggesting large-scale segmental duplication events in evolution. Substantial expansion of light-harvesting genes encoding fucoxanthin-chlorophyll a/c binding proteins, as well as expansion of photoreceptor gene families encoding aureochromes and cyptochromes (CRY) in S. marinoi were found, which may have shaped ecological adaptation of S. marinoi. In conclusion, the construction of the first high-quality Skeletonema genome assembly offers valuable clues on the ecological and evolutionary characteristics of this dominant coastal diatom species.
菱形藻属的硅藻种是全球沿海水域的优势种，在海洋初级生产和全球生物地球化学循环中起着重要作用。许多菱形藻种也被广泛研究，因为它们可以引发有害藻华（HAB），对海洋生态系统和水产养殖产生负面影响。在本研究中，构建了菱形藻的首个染色体水平基因组组装。该基因组大小为 64.99 Mb，具有 1.95 Mb 的 contig N50。多达 97.12%的 contigs成功锚定在 24 条染色体上。对注释基因的分析表明，在 S. marinoi 基因组中存在 28 个大的共线性块，包含 2397 个共线性基因对，表明在进化过程中发生了大规模的片段重复事件。在 S. marinoi 中发现了大量扩展的光捕获基因，编码褐藻黄素-叶绿素 a/c 结合蛋白，以及扩展的光受体基因家族，编码 aureochromes 和 cryptochromes (CRY)，这可能塑造了 S. marinoi 的生态适应。总之，首个高质量的菱形藻基因组组装的构建为该优势沿海硅藻种的生态和进化特征提供了有价值的线索。
