First Whole Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota).
First Whole Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota).
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DOI：
10.1093/gbe/evad074
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发表时间：
2023-05-07
影响因子：
3.3
通讯作者：
Gaya, Ester
中科院分区：
文献类型：
--
作者：
Llewellyn, Theo;Mian, Sahr;Hill, Rowena;Leitch, Ilia J.;Gaya, Ester
地衣真菌是一类多样的、具有重要生态意义的专性互惠共生体。由于在培养中维持它们的困难和它们极其缓慢的生长，地衣学家越来越多地选择宏基因组测序，然后使用生物信息学管道进行共生体基因组分离。然而，在不知道地衣形成真菌的真实基因组大小的情况下，我们不能量化基因组组装的完整性和生物信息学过滤的功效。为了解决这个问题，我们在这里报告了地衣形成真菌Ramalina farinacea（L.）啊。使用Oxford Nanopore长读技术进行测序，同时使用流式细胞术直接测量其基因组大小。组装显示出高的邻接性（N50 = 1.55 Mb）和基因集完整性（BUSCO = 95.8%）。 获得的33.61 Mb/1C的高度稳健的基因组大小（变异系数= 2.98）表明我们的组装覆盖了整个基因组的97%。我们的研究结果表明，准确的基因组大小的测量可以直接从地衣菌体和用于提供一个基准，用于评估真正的细胞学完整性的宏基因组衍生的组件。
Lichen-forming fungi are a diverse and ecologically important group of obligate mutualistic symbionts. Due to difficulties with maintaining them in culture and their extremely slow growth, lichenologists are increasingly opting for metagenomic sequencing followed by symbiont genome separation using bioinformatic pipelines. However, without knowing the true genome size of the lichen-forming fungus, we cannot quantify the completeness of the genome assembly and the efficacy of the bioinformatic filtering. To address this issue, we report here the first whole-genome assembly for the lichen-forming fungus Ramalina farinacea (L.) Ach. sequenced with Oxford Nanopore long-read technology alongside direct measurements of its genome size using flow cytometry. The assembly showed high contiguity (N50 = 1.55 Mb) and gene set completeness (BUSCO = 95.8%). The highly robust genome size of 33.61 Mb/1C (coefficients of variation = 2.98) that was obtained showed our assembly covered 97% of the entire genome. Our results demonstrate that accurate genome size measurements can be obtained directly from lichen thalli and used to provide a benchmark for assessing true cytometric completeness of metagenome-derived assemblies.
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影响因子：
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通讯作者：
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作者：
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通讯作者：
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