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Klebsiella bacteriophage phage Przondovirus sequencing assembly

HYPPA - a hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Abstract ID: 96-UP

Claire K. A. Elek 1,2*, Teagan L. Brown 1, Thanh Le Viet 1, Rhiannon Evans 1, Dave J. Baker 1, Andrea Telatin 1, Sumeet K. Tiwari 1, Haider Al-Khanaq 1, Gaëtan Thilliez 1, Robert A. Kingsley 1, Lindsay J. Hall 1,2,3, Mark A. Webber 1,2, Evelien M. Adriaenssens 1

  1. Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
  2. University of East Anglia, Norwich Research Park, Norwich, UK
  3. Chair of Intestinal Microbiome, ZIEL—Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany

Bacteriophages (phages) within the Przondovirus genus are T7-like podoviruses belonging to the Studiervirinae subfamily, within the Autographiviridae family and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, 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 data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.