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 Halobacterium 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 cow hide (91-R6 T , epithet "salinaria," the type strain of Hbt. 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 five 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 twentieth-century isolate 63-R2 is the immediate ancestor of the twin laboratory strains NRC-1 and R1.

In Silico Prophage Analysis of Halobacterium salinarum ATCC 33170

“…However, dissimilarities in genome-wide insertion-deletion rates and mutation spectra suggest unique evolutionary pathways. Notably, H. salinarum is characterized by a high rate of spontaneous mutations attributed to mobile genetic elements (MGEs), including ISH elements and transposons [64,65]. Studied since the 1980s, these elements are associated with the insertional inactivation of genes, as well as genome inversions and rearrangements.…”

“…Studied since the 1980s, these elements are associated with the insertional inactivation of genes, as well as genome inversions and rearrangements. For example, differences between laboratory strains NRC-1 and R1 primarily stem from the dynamic mobilome, exemplifying the impact of MGEs on the evolutionary landscape of H. salinarum [65].…”

One Advantage of Being Polyploid: Prokaryotes of Various Phylogenetic Groups Can Grow in the Absence of an Environmental Phosphate Source at the Expense of Their High Genome Copy Numbers

“…H. salinarum was isolated 100 years ago from salted fish [ 40 ]. This isolate was subsequently lost, and the type strains that are used today were isolated in 1934 from salted animal hides [ 41 ]. H. salinarum contains the four retinal proteins bacteriorhodopsin, halorhodopsin, and sensory rhodopsins I and II, which have been intensively studied [ 42 , 43 , 44 , 45 ].…”