Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, and horizontal gene transfer. Despite recent progress in viral metagenomics, the inherent genetic complexity of virus populations still poses technical difficulties for recovering complete virus genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach enabling direct recovery of complete viral genome sequences from environmental samples. Our method yielded thousands of full-length, high-quality draft virus genome sequences that were not recovered using standard short-read assembly approaches. Additionally, our analyses discriminated between populations whose genomes had identical direct terminal repeats, versus those with circularly permuted repeats at their termini, thus providing new insight into native virus reproduction and genome packaging. Novel DNA sequences were discovered whose repeat structures, gene contents, and concatemer lengths suggest they are phage-inducible chromosomal islands, which are packaged as concatemers in phage particles, with lengths that match the size ranges of co-occurring phage genomes. Our new virus sequencing strategy can provide previously unavailable information about the genome structures, population biology, and ecology of naturally occurring viruses and viral parasites.

中文翻译：

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免组装的单分子测序可从天然微生物群落中恢复完整的病毒基因组。

病毒是地球上最丰富的生物实体，在宿主生态，进化和水平基因转移中起关键作用。尽管最近在病毒宏基因组学方面取得了进展，但是病毒种群固有的遗传复杂性仍然给从自然种群中恢复完整病毒基因组带来了技术难题。为了应对这些挑战，我们开发了一种无装配的单分子纳米孔测序方法，可从环境样品中直接回收完整的病毒基因组序列。我们的方法产生了数千个全长，高质量的草案病毒基因组序列，这些序列使用标准的短读组装方法无法回收。此外，我们的分析区分了基因组具有相同直接末端重复序列的人群，与那些在末端具有圆形排列重复序列的序列相比，从而提供了对天然病毒繁殖和基因组包装的新见解。发现了新的DNA序列，其重复结构，基因含量和连接体长度表明它们是噬菌体可诱导的染色体岛，它们被包装成连接体形式的噬菌体颗粒，其长度与共生噬菌体基因组的大小范围相匹配。我们的新病毒测序策略可以提供有关自然存在的病毒和病毒寄生虫的基因组结构，种群生物学以及生态学的以前不可用的信息。它们以串联体的形式包装在噬菌体颗粒中，其长度与共生噬菌体基因组的大小范围相匹配。我们的新病毒测序策略可以提供有关自然存在的病毒和病毒寄生虫的基因组结构，种群生物学以及生态学的以前不可用的信息。它们以串联体的形式包装在噬菌体颗粒中，其长度与共生噬菌体基因组的大小范围相匹配。我们的新病毒测序策略可以提供有关自然存在的病毒和病毒寄生虫的基因组结构，种群生物学以及生态学的以前不可用的信息。