Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1

Abstract

Halobacterium salinarum is an extremely halophilic archaeon that is widely distributed in hypersaline environments and was originally isolated as a spoilage organism of salted fish and hides. The type strain 91-R6 (DSM 3754 T ) has seldom been studied and its genome sequence has only recently been determined by our group. The exact relationship between the type strain and two widely used model strains, NRC-1 and R1, has not been described before. The genome of Hbt. salinarum strain 91-R6 consists of a chromosome (2.17 Mb) and two large plasmids (148 and 102 kb, with 39,230 bp being duplicated). Cytosine residues are methylated ( m4 C) within CTAG motifs. The genomes of type and laboratory strains are closely related, their chromosomes sharing average nucleotide identity (ANIb) values of 98% and in silico DNA-DNA hybridization (DDH) values of 95%. The chromosomes are completely colinear, do not show genome rearrangement, and matching segments show <1% sequence difference. Among the strain-specific sequences are three large chromosomal replacement regions (>10 kb). The well-studied AT-rich island (61 kb) of the laboratory strains is replaced by a distinct AT-rich sequence (47 kb) in 91-R6. Another large replacement (91-R6: 78 kb, R1: 44 kb) codes for distinct homologs of proteins involved in motility and N-glycosylation. Most (107 kb) of plasmid pHSAL1 (91-R6) is very closely related to part of plasmid pHS3 (R1) and codes for essential genes (e.g. arginine-tRNA ligase and the pyrimidine biosynthesis enzyme aspartate carbamoyltransferase). Part of pHS3 (42.5 kb total) is closely related to the largest strain-specific sequence (164 kb)in the type strain chromosome. Genome sequencing unraveled the close relationship between the Hbt. salinarum type strain and two well-studied laboratory strains at the DNA and protein levels. Although an independent isolate, the type strain shows a remarkably low evolutionary difference to the laboratory strains. K E Y W O R D Scomparative genomics, genomic variability, haloarchaea, halobacteria, megaplasmid, type strain 2 of 44 | PFEIFFER Et al.

Comparative Genomics of Two New HF1-like Haloviruses

“…More subtle, non-palindromic motifs may also be avoided by HF1-group viruses but were not focused upon in this study. For example, the BREX defence system [41] is widespread among haloarchaea [42] and uses non-palindromic 6mer-motifs to recognize foreign DNA.…”

Functionalized Membrane Domains: An Ancestral Feature of Archaea?

“…Pyrococcus species were all grown at 98 • C, whereas Palaeococcus and Thermococcus species were grown at 85 • C, with the exception of Thermococcus piezophilus and Thermococcus sibiricus, which were grown at 75 • C. Before growth, the medium was reduced by adding Na 2 S (0.1% final concentration). To confirm the assumptions based on our literature survey, additional strains were grown under their respective optimal conditions and included: Aciduliprofundum boonei DSM19572 (Reysenbach et al, 2006), Aeropyrum pernix DSM11879 (Sako et al, 1996), Halobacterium salinarum DSM3754 (Pfeiffer et al, 2019), Haloferax volcanii DSM3757 (Torreblanca et al, 1986), Methanothermobacter thermautotrophicus DSM1053 (Schönheit et al, 1980), Methanocaldococcus jannaschii DSM2661 (Jones et al, 1983), Natronomonas pharaonis DSM2160 (Tindall et al, 1984), Pyrobaculum islandicum DSM4184 (Huber et al, 1987), and Sulfolobus acidocaldarius DSM639 (Langworthy et al, 1974). Growth was monitored by counting with a Thoma cell, and growth curves were established for each species.…”

Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

“…All replicons had at least 115-fold mean coverage. Illumina sequencing was used to validate and, if required, correct the assembled genome sequence, as described in Section “Material and Methods.” This followed an established procedure ( Pfeiffer et al, 2020 ).…”