Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing

Chen, J.; Sun, C.; Dong, Y.; Jin, M.; Lai, S.; Jia, L.; Zhao, X.; Wang, H.; Gao, N.L.; Bork, P.; Liu, Z.; Chen, W.H.; Zhao, X.M.

Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing

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Item Type:	Article
Title:	Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing
Creators Name:	Chen, J., Sun, C., Dong, Y., Jin, M., Lai, S., Jia, L., Zhao, X., Wang, H., Gao, N.L., Bork, P., Liu, Z., Chen, W.H. and Zhao, X.M.
Abstract:	Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.
Keywords:	crAssphage, Gubaphage, Gut Virome, Long-Read Sequencing, pacBio Sequel II, Terminase, Virus-Like Particle
Source:	Advanced Science
ISSN:	2198-3844
Publisher:	Wiley
Volume:	11
Number:	13
Page Range:	2305818
Date:	3 April 2024
Official Publication:	https://doi.org/10.1002/advs.202305818
PubMed:	View item in PubMed

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