Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing

• DOI: 10.1038/s42003-024-05998-w
• Publication Date: 2024-03-27T11:10:03Z
• Authors: Sachiko Masuda; Pamela Gan; Yuya Kiguchi; Mizue Anda; Kazuhiro Sasaki; Arisa Shibata; Wataru Iwasaki; Wataru Suda; Ken Shirasu
• Keywords: Phyllosphere

Abstract The plant microbiome is crucial for growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location these genes on chromosomes or plasmids. To gain insights into makeup rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled 26,067 contigs including 142 circular Within contigs, 669 complete 16S rRNA clustered 166 species, 121 which show low identity (<97%) to defined sequences, suggesting novel species. contain megaplasmid, most smaller plasmids bacteriophages. One contig represents chromosome difficult-to-culture bacterium Candidatus Saccharibacteria . Our findings demonstrate efficacy long-read-based metagenomics profiling microbial communities discovering sequences plant-microbiome studies.