Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case

PeerJ

article

Mami Tanaka¹  Sayaka Mino¹  Yoshitoshi Ogura²  Tetsuya Hayashi²  Tomoo Sawabe¹ 

[1] Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University;Department of Bacteriology, Faculty of Medical Sciences, Kyushu University

关键词: Vibrionaceae;    Genome taxonomy;    Nanopore;   

DOI  :  10.7717/peerj.5018

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

【 授权许可】

CC BY