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Genome comparison reveals that Halobacterium salinarum 63-R2 is the origin of the twin laboratory strains NRC-1 and R1
  • Friedhelm Pfeiffer,
  • Mike Dyall-Smith
Friedhelm Pfeiffer
Max-Planck-Institut fur Biochemie

Corresponding Author:[email protected]

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Mike Dyall-Smith
Max-Planck-Institut fur Biochemie
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The genome of Halobacterium strain 63-R2 was recently reported and provides the opportunity to resolve long-standing issues regarding the source of two widely used model strains of Hbt. salinarum, NRC-1 and R1. Strain 63-R2 was isolated in 1934 from a salted buffalo hide (epithet ‘cutirubra’), along with another strain from a salted cowhide (91-R6T, epithet ‘salinaria’, the type strain of Halobacterium salinarum). Both strains belong to the same species according to genome-based taxonomy analysis (TYGS), with chromosome sequences showing 99.64% identity over 1.85 Mb. The chromosome of strain 63-R2 is 99.99% identical to the two laboratory strains NRC-1 and R1, with only 5 indels, excluding the mobilome. The two reported plasmids of strain 63-R2 share their architecture with plasmids of strain R1 (pHcu43/pHS4, 99.89% identity; pHcu235/pHS3, 100.0% identity). We detected and assembled additional plasmids, using PacBio reads deposited at the SRA database, further corroborating that strain differences are minimal. One plasmid, pHcu190 (190,816 bp) corresponds to pHS1 (strain R1) but is even more similar in architecture to pNRC100 (strain NRC-1). Another plasmid, pHcu229, assembled partially and completed in silico (229,124 bp), shares most of its architecture with pHS2 (strain R1). In deviating regions, it corresponds to pNRC200 (strain NRC-1). Further architectural differences between the laboratory strain plasmids are not unique but are present in strain 63-R2, which contains characteristics from both of them. Based on these observations, it is proposed that the early 20th-century isolate 63-R2 is the immediate ancestor of the twin laboratory strains NRC-1 and R1.
06 Nov 2022Submitted to MicrobiologyOpen
07 Nov 2022Submission Checks Completed
07 Nov 2022Assigned to Editor
17 Nov 2022Reviewer(s) Assigned
13 Feb 2023Review(s) Completed, Editorial Evaluation Pending
14 Feb 2023Editorial Decision: Revise Minor
04 Apr 20231st Revision Received
06 Apr 2023Assigned to Editor
06 Apr 2023Submission Checks Completed
12 Apr 2023Review(s) Completed, Editorial Evaluation Pending
13 Apr 2023Reviewer(s) Assigned
04 May 2023Editorial Decision: Revise Minor
09 May 20232nd Revision Received
10 May 2023Assigned to Editor
10 May 2023Submission Checks Completed
11 May 2023Review(s) Completed, Editorial Evaluation Pending
13 May 2023Editorial Decision: Accept