Genome comparison reveals that Halobacterium salinarum 63-R2 is the
origin of the twin laboratory strains NRC-1 and R1
Abstract
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.