CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266200, China.
Sci Data. 2024 Apr 20;11(1):403. doi: 10.1038/s41597-024-03238-8.
Skeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and high-throughput chromatin conformation capture. The assembled genome has a size of 78.78 Mb with a scaffold N50 of 3.17 Mb, anchored to 23 pseudo-chromosomes. In total, 20,613 protein-coding genes were predicted, of which 17,757 (86.14%) genes were functionally annotated. Collinearity analysis of the genomes of S. tropicum and S. marinoi revealed that these two genomes were highly homologous. This chromosome-level genome assembly of S. tropicum provides a valuable genomic platform for comparative analysis of mechanisms of ecological adaption.
热带骨条藻是骨条藻属的一种海洋硅藻，该属还包括许多著名的物种，包括 S. marinoi。热带骨条藻是一种喜高温的物种，在热带海洋或温带海洋地区的夏季和秋季繁盛。然而，热带骨条藻的生态适应机制仍知之甚少，部分原因是缺乏高质量的全基因组组装。在这里，我们使用 PacBio 单分子测序和高通量染色质构象捕获等前沿技术，报告了热带骨条藻的第一个高质量染色体尺度基因组组装。组装的基因组大小为 78.78 Mb，支架 N50 为 3.17 Mb，锚定在 23 个假染色体上。总共预测了 20613 个蛋白质编码基因，其中 17757 个（86.14%）基因具有功能注释。热带骨条藻和 S. marinoi 基因组的共线性分析表明，这两个基因组高度同源。热带骨条藻的这种染色体水平的基因组组装为生态适应机制的比较分析提供了一个有价值的基因组平台。
