Elek Claire K A, Brown Teagan L, Le Viet Thanh, Evans Rhiannon, Baker David J, Telatin Andrea, Tiwari Sumeet K, Al-Khanaq Haider, Thilliez Gaëtan, Kingsley Robert A, Hall Lindsay J, Webber Mark A, Adriaenssens Evelien M
Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK.
University of East Anglia, Norwich Research Park, Norwich, UK.
Microb Genom. 2023 Jul;9(7). doi: 10.1099/mgen.0.001065.
Bacteriophages (phages) within the genus are T7-like podoviruses belonging to the subfamily , within the family 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 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.
属内的噬菌体（phages）是属于科内亚科的T7样短尾病毒，具有高度保守的基因组结构。这些噬菌体的基因组大小在37至42 kb之间，编码50至60个基因，其特征是线性染色体两侧存在直接末端重复序列（DTRs）。在仅短读长和混合组装过程中，这些DTRs常常会被删除。此外，仅长读长组装常常充斥着测序和/或组装错误，需要额外的整理。在这里，我们展示了针对 spp. 的十种新型przondovirus的分离和特性描述。我们描述了HYPPA，一种混合和多轮抛光噬菌体组装工作流程，它利用长读长组装结合短读长测序来解析噬菌体DTRs并纠正错误，无需费力的引物步移和桑格测序验证。我们的组装工作流程使用牛津纳米孔技术进行长读长测序，因为其易获取性，使其成为目前更相关的长读长测序技术，使用Illumina DNA Prep进行短读长测序，这代表了全球最常用的技术。我们的数据证明了在发表之前以及将其用于比较基因组学之前，仔细整理噬菌体组装的重要性。
