美国农业部Timothy P. L. Smith、加州大学旧金山分校Pavel A. Pevzner等研究人员合作从复杂微生物群落中生成谱系分辨率的完整元基因组组装基因组。这一研究成果于2022年1月3日在线发表在国际学术期刊《自然—生物技术》上。
Author: Bickhart, Derek M., Kolmogorov, Mikhail, Tseng, Elizabeth, Portik, Daniel M., Korobeynikov, Anton, Tolstoganov, Ivan, Uritskiy, Gherman, Liachko, Ivan, Sullivan, Shawn T., Shin, Sung Bong, Zorea, Alvah, Andreu, Victria Pascal, Panke-Buisse, Kevin, Medema, Marnix H., Mizrahi, Itzhak, Pevzner, Pavel A., Smith, Timothy P. L.
Issue&Volume: 2022-01-03
Abstract: Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host–viral (host–plasmid) associations using Hi-C data.
DOI: 10.1038/s41587-021-01130-z
Source: https://www.nature.com/articles/s41587-021-01130-z
Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex
本期文章：《自然—生物技术》：Online/在线发表
