Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden.
Department of Cell and Molecular Biology, Uppsala University, and Microbial Single Cell Genomics Facility, Science for Life Laboratory, Uppsala, Sweden.
Sci Rep. 2020 Jan 28;10(1):1303. doi: 10.1038/s41598-020-58025-3.
The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.
新型测序技术的出现揭示了地球上巨大的多样性。基因组数据使我们能够了解我们原本不知道存在的生物体的生态和功能。然而，仍然存在重大的方法学挑战，特别是对于具有大型基因组的多细胞生物。丛枝菌根（AM）真菌是重要的植物共生体，具有隐蔽和复杂的多细胞生命周期，因此是开发方法的合适模型系统。在这里，我们报告了一种用于大规模、无偏核分选、测序和从头组装 AM 真菌基因组的新方法。在对三种组装工作流程进行比较分析后，我们讨论了如何最好地使用来自单个核的序列数据进行不同的下游分析，如系统发育基因组学和单个核的比较基因组学。基于对完整性的分析，我们得出结论，从六个到七个核可以产生全面的从头基因组组装。该方法具有广泛的适用性，将极大地提高我们研究具有复杂生命周期的多细胞真核生物的能力。
