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项目编号 PRJCA008836
项目标题 The DNA methylation landscape of human gut phageome
涉及领域 Medical
数据类型 Whole genome sequencing
物种名称 human viral metagenome
描述信息 DNA methylation is essential for the survival of bacteriophages. Yet, we know little about the methylation of their genomes. Here, we analyze the methylomes of 9,665 metagenome-assembled high-quality human gut phages using single-molecule real-time sequencing. We show that DNA methylation is universal, affecting 95.68% of the phages. We identify over nine million non-redundant methylation sites and 973 motifs in these genomes, and reveal distinctive patterns of N4-methyl-cytosine (m4C) and N6-methyl-adenine (m6A) modifications attributable to genomic regions, gene functions, and phage lifestyles. Strikingly, 33.9% of the phages encode their own DNA methyltransferases (MTases) that contribute to genome methylation; consequently, both the methylation sites and motifs increase with the increasing copy of MTases. Restriction enzyme (REase) genes are also found in 23% of the phages and distribute mutual-exclusively with the MTases. Phage lifestyles strongly affect the distributions of these genes; in particular, temperate phages prefer MTases, while virulent ones prefer REases. Most of the MTases and REases are of bacterial/archaeal origin, and can link 12.35% phages to their hosts with 92% specificity at the species level. Our results suggest that transfer of functional genes significantly impact phage fitness and can be exploited to link more phages to their hosts with high specificity.
样品范围 Environment
发布日期 2023-04-04
出版信息
PubMed ID 文章标题 杂志名称 Doi 发表年份
39707560 Complementary insights into gut viral genomes: a comparative benchmark of short-and long-Read metagenomes using diverse assemblers and binners Microbiome 10.1186/s40168-024-01981-z 2024
37382405 Long‐Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage‐Encoded Methyltransferases Advanced Science 10.1002/advs.202302159 2023
项目资金来源
机构 项目类型 授权项目ID 授权项目名称
National Key Research and Development Program of China 2020YFA0712403
National Natural Science Foundation of China (NSFC) 61932008
National Natural Science Foundation of China (NSFC) 61772368
National Natural Science Foundation of China (NSFC) 32070660
National Natural Science Foundation of China (NSFC) 31770132
National Natural Science Foundation of China (NSFC) 81873969
提交者 Wei-Hua Chen (weihuachen@hust.edu.cn)
提交单位 Huazhong University of Science and Technology
提交日期 2022-03-25

项目包含数据信息

资源名称 描述
BioSample (104)  show -
GSA (1) -
CRA006494 The DNA methylation landscape of human gut phageome