Chromosome-Scale Genome Assembly of the Marine Oleaginous Diatom Fistulifera solaris
Chromosome-Scale Genome Assembly of the Marine Oleaginous Diatom Fistulifera solaris
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DOI：
10.1007/s10126-022-10147-7
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发表时间：
2022-08
影响因子：
3
通讯作者：
Yoshiaki Maeda;R. Kobayashi;Kahori Watanabe;T. Yoshino;C. Bowler;M. Matsumoto;Tsuyoshi Tanaka
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文献类型：
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作者：
Yoshiaki Maeda;R. Kobayashi;Kahori Watanabe;T. Yoshino;C. Bowler;M. Matsumoto;Tsuyoshi Tanaka
包括硅藻的微藻对于环境友好的制造例如生物燃料、化学品和材料的生产是有意义的。高含油性的海洋浮游植物Fistulifera solarishas被研究为用于这些应用的有前途的宿主生物。最近报道的大规模基因工程的基础上附加型载体的硅藻可能是有用的，以进一步提高的潜力。solaris，而我们需要更多地了解硅藻着丝粒的作用模式，以合理地设计用于稳定的染色体外维持的附加型载体。我们先前使用焦磷酸测序（短读段测序）的基因组分析已经产生了片段化的支架，其对于预测每条染色体上的着丝粒是无用的。在这里，我们报告了几乎完整的染色体结构的基因组ofF。使用长读段纳米孔测序平台MinION的Solomon。仅使用MinION流动池进行一次运行，就实现了44条染色体中的41条染色体的染色体规模组装，端粒到端粒分辨率。从16条染色体中预测了推定的着丝粒区域，并且我们在预测的着丝粒中发现了推定的一致基序。在模式硅藻中进行了相似模体搜索，但没有发现一致模体，因此，这是首次成功估计硅藻着丝粒中一致模体的研究。染色体规模的组装也表明可能存在多拷贝的小染色体和串联重复的脂肪生成基因与产油表型有关。solaris。本研究的结果有助于理解和进一步工程化F. solaris。
Microalgae including diatoms are of interest for environmentally friendly manufacturing such as production of biofuels, chemicals, and materials. The highly oil-accumulating marine diatomFistulifera solarishas 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 ofF. 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 ofF. solarisusing 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 ofF. solaris. Findings of this study are useful to understand and further engineer the oleaginous phenotype ofF. solaris.