Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes

Abstract

Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors

“…Core genome-based phylogeny is a relatively new proposed method of classification of genomes, which is consistent with MLST in other studies [ 10 , 14 ]. As previously reported, ANI and dDDH calculations could confirm these variations [ 15 ]. In ANI variation and dDDH analyses, when compared with the reference genome ATCC7966, all the core genomes showing variation were already classified into different phylogenetic clusters.…”

“…The functional annotation of COG and KEGG databases to infer the functions of proteins is also of great concern [ 15 , 25 , 26 ], as they categorize the varying fractions into families and superfamilies. Based on both COG and KEGG database assignment results, the core genome was enriched in metabolism-related genes, while dispensable genes were found to be higher among the motility, cell communication and defence mechanisms.…”

“…This technique is also being used to identify mutations and microevolution among the constantly evolving genes [ 14 ]. Identification and distribution of virulence factors, bacteriophages, and antibiotic resistance genes among geographically isolated strains are important features of WGS [ 15 ]. Application of WGS to epidemiology has created an opportunity to correctly diagnose disease caused by A. hydrophila and has been helpful in outbreak investigation [ 10 ].…”

Horizontal Gene Transfer in Thermus spp.

“…Small plasmids <20 kbp are also found in different strains (Tripathi et al, 2017 around 200 kbp named pTT27 in the strains HB27 and HB8 (Ohtani et al, 2012). Although the pTT27related megaplasmids of T. thermophilus and other Thermus spp concentrate "dispensable" genes, they also encode complete or partial housekeeping pathways, including the synthesis of relevant compounds such as carotenes, coenzyme B12, dATP, dGTP and dUTP, and siroheme (Henne et al, 2004) (Tripathi et al, 2017). Those Thermus isolates lacking a pTT27-like megaplasmid encode these housekeeping genes within different regions of the chromosome (Brumm et al, 2015;Fujino et al, 2017;Gounder et al, 2011).…”

“…The average genome size is about 2.3 Mbp, which in most strains is divided between a chromosome of around 2 Mbp (containing the core genome conserved among all strains in the species) and one or more megaplasmids ranking from 60 to 440 kbp that harbors strain-specific genes and thus, showing lower synteny among isolates (Bruggemann and Chen, 2006). Small plasmids <20 kbp are also found in different strains (Tripathi et al, 2017 around 200 kbp named pTT27 in the strains HB27 and HB8 (Ohtani et al, 2012). Although the pTT27related megaplasmids of T. thermophilus and other Thermus spp concentrate "dispensable" genes, they also encode complete or partial housekeeping pathways, including the synthesis of relevant compounds such as carotenes, coenzyme B12, dATP, dGTP and dUTP, and siroheme (Henne et al, 2004) (Tripathi et al, 2017).…”