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- Title
Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.
- Authors
Masuda, Sachiko; Gan, Pamela; Kiguchi, Yuya; Anda, Mizue; Sasaki, Kazuhiro; Shibata, Arisa; Iwasaki, Wataru; Suda, Wataru; Shirasu, Ken
- Abstract
The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled into 26,067 contigs including 142 circular sequences. Within these contigs, 669 complete 16S rRNA genes are clustered into 166 bacterial species, 121 of which show low identity (<97%) to defined sequences, suggesting novel species. The circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs are defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of a difficult-to-culture bacterium Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies. The long-read metagenome of rice phyllosphere microbiome shows novel complete chromosomes, plasmids, bacteriophages, and novel bacterial species. Notably one complete chromosome belongs to the difficult-to-culture bacterium CandidatusSaccharibacteria.
- Subjects
METAGENOMICS; LOCUS (Genetics); BACTERIAL chromosomes; CHROMOSOMES; MICROBIAL communities
- Publication
Communications Biology, 2024, Vol 7, Issue 1, p1
- ISSN
2399-3642
- Publication type
Article
- DOI
10.1038/s42003-024-05998-w