Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Koganei, Tokyo, 184-8588, Japan.
Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan.
Mar Biotechnol (NY). 2022 Aug;24(4):788-800. doi: 10.1007/s10126-022-10147-7. Epub 2022 Aug 2.
Microalgae including diatoms are of interest for environmentally friendly manufacturing such as production of biofuels, chemicals, and materials. The highly oil-accumulating marine diatom Fistulifera solaris has been studied as a promising host organism to be employed for these applications. Recently reported large-scale genetic engineering based on episomal vectors for diatoms could be useful to further enhance the potential of F. solaris, whereas we need to understand more the mode-of-action of diatom centromeres to rationally design the episomal vectors for stable extrachromosomal maintenance. Our previous genome analysis with pyrosequencing (short read sequencing) had generated the fragmented scaffolds which were not useful to predict centromeres on each chromosome. Here, we report the almost complete chromosomal structure of the genome of F. solaris using a long-read nanopore sequencing platform MinION. From just one single run using a MinION flow-cell, the chromosome-scale assembly with telomere-to-telomere resolution was achieved for 41 out of 44 chromosomes. Putative centromere regions were predicted from the 16 chromosomes, and we discovered putative consensus motifs in the predicted centromeres. Similar motif search had been performed in model diatoms, but no consensus motif was found. Therefore, this is the first study to successfully estimate consensus motifs in diatom centromeres. The chromosome-scale assembly also suggests the potential existence of multi-copy mini-chromosomes and tandemly repeated lipogenesis genes related to the oleaginous phenotype of F. solaris. Findings of this study are useful to understand and further engineer the oleaginous phenotype of F. solaris.
微藻（包括硅藻）在环境友好型制造方面具有重要意义，例如生物燃料、化学品和材料的生产。富含油脂的海洋硅藻 Fistulifera solaris 已被研究作为一种很有前途的宿主生物，用于这些应用。最近报道的基于附加体载体的大规模基因工程对于进一步增强 F. solaris 的潜力可能是有用的，然而，我们需要更多地了解硅藻着丝粒的作用模式，以便合理设计用于稳定染色体外维持的附加体载体。我们之前使用焦磷酸测序（短读测序）进行的基因组分析生成了不便于预测每条染色体着丝粒的片段化支架。在这里，我们使用长读长纳米孔测序平台 MinION 报告了 F. solaris 基因组的几乎完整的染色体结构。仅使用 MinION 流池进行一次运行，就实现了 44 条染色体中的 41 条染色体的端到端分辨率的染色体级别的组装。从 16 条染色体中预测了假定的着丝粒区域，并且我们在预测的着丝粒中发现了假定的共识基序。在模式硅藻中进行了类似的基序搜索，但没有发现共识基序。因此，这是首次成功估计硅藻着丝粒中共识基序的研究。染色体级别的组装还表明，多拷贝微染色体和与 F. solaris 油脂表型相关的串联重复脂生成基因可能存在。这项研究的结果有助于理解和进一步工程化 F. solaris 的油脂表型。
