Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐ and Long‐Read Sequencing

Author:

Chen Jingchao1,Sun Chuqing1,Dong Yanqi2,Jin Menglu13,Lai Senying2,Jia Longhao2,Zhao Xueyang3,Wang Huarui1,Gao Na L.14,Bork Peer5678,Liu Zhi9,Chen Wei‐Hua1310ORCID,Zhao Xing‐Ming2111213

Affiliation:

1. Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular Imaging Center for Artificial Intelligence Biology Department of Bioinformatics and Systems Biology College of Life Science and Technology Huazhong University of Science and Technology Wuhan Hubei 430074 China

2. Department of Neurology Zhongshan Hospital and Institute of Science and Technology for Brain‐Inspired Intelligence Fudan University Shanghai 200433 China

3. College of Life Science Henan Normal University Xinxiang Henan 453007 China

4. Department of Laboratory Medicine Zhongnan Hospital of Wuhan University Wuhan University Wuhan 430071 China

5. European Molecular Biology Laboratory Structural and Computational Biology Unit 69117 Heidelberg Germany

6. Max Delbrück Centre for Molecular Medicine 13125 Berlin Germany

7. Yonsei Frontier Lab (YFL) Yonsei University 03722 Seoul South Korea

8. Department of Bioinformatics Biocenter University of Würzburg 97070 Würzburg Germany

9. Department of Biotechnology College of Life Science and Technology Huazhong University of Science and Technology 430074 Wuhan China

10. Institution of Medical Artificial Intelligence Binzhou Medical University Yantai 264003 China

11. MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence and MOE Frontiers Center for Brain Science Fudan University Shanghai 200433 China

12. State Key Laboratory of Medical Neurobiology Institute of Brain Science Fudan University Shanghai 200433 China

13. International Human Phenome Institutes (Shanghai) Shanghai 200433 China

Abstract

AbstractCurrent 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.

Funder

National Natural Science Foundation of China

National Key Research and Development Program of China

Publisher

Wiley

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