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bioRxiv · 10.1101/2025.05.25.655001

Whole-genome sequencing of diverse 351 cultured prokaryotes including yet-unsequenced fastidious type strains

Kato, S.·Masuda, S.·Shibata, A.·Itoh, T.·Sakamoto, M.·Shirasu, K.·Ohkuma, M.
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Abstract

Genome sequences provide fundamental information for both basic and applied life sciences. Whole-genome sequencing is now requested for describing novel prokaryotic species and designating their type strains, which serve as representative and well-characterized strains of the species. Indeed, the number of sequenced prokaryotic genomes has been rapidly increasing. However, a considerable number of isolated strains, particularly "fastidious" type strains such as strict anaerobes and slow growers, remain without genome sequence information. Here we report the whole-genome sequencing of 290 bacterial and 61 archaeal strains, including fastidious type strains, obtained from Japan Collection of Microorganisms (JCM) using a combination of short- and long-read sequencing technologies. The dataset includes 284 type strain genomes and 235 complete genomes. Notably, in the dataset, genomes of over 200 strains, including over 150 type strains, had not been made publicly available. Comparative genomic analysis suggests that some strains need to be assigned to novel taxa or reclassified. Functional gene survey indicates that some strains possess previously unrecognized potential for carbon fixation or bioactive secondary metabolite production. Our dataset will contribute to more accurate taxonomic classification, fill gaps in the phylogeny of prokaryotes, and provide insights into their physiology and ecology.

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Kato, S., Masuda, S., Shibata, A., Itoh, T., Sakamoto, M., Shirasu, K., Ohkuma, M.. 2025-05-27. Whole-genome sequencing of diverse 351 cultured prokaryotes including yet-unsequenced fastidious type strains. https://doi.org/10.1101/2025.05.25.655001

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