PDF(Pubmed)
Abstract：
Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.
摘要：
Przondovirus属中的噬菌体（噬菌体）是属于Studiervirinae亚科的T7样podovirus，在自拟病毒科中，并且具有高度保守的基因组组织。这些噬菌体的基因组大小从37到42kb，编码50-60个基因,其特征在于存在线性染色体侧翼的直接末端重复(DTR)。这些DTR通常在短只读和混合组装期间被删除。此外，长只读组件通常会出现测序和/或组装错误，需要额外的管理。这里,我们介绍了十种针对克雷伯菌属的新型przondovirus的分离和表征。我们描述了HYPPA，混合和聚波兰噬菌体组装工作流程，它利用长读取组件与短读取测序相结合来解析噬菌体DTR并纠正错误，否定了费力的引物行走和Sanger测序验证的需要。我们的组装工作流程利用牛津纳米孔技术进行长读取测序，使其成为目前更相关的长读数测序技术，和IlluminaDNA准备进行短读测序，代表全球最常用的技术。我们的数据证明了在发表之前仔细管理噬菌体组装的重要性，在将它们用于比较基因组学之前。
