Comparative genomics of the highly halophilic Haloferacaceae

Abstract

The Haloferacaceae are a family of extremely halophilic archaea with many species producing enzymes and products beneficial for industrial biotechnology. They are, however, relatively under-characterised with regards to genetics and gene products. This study aims to use existing sequence data to highlight genetic diversity, create pangenomes for three genera, and provide secondary metabolite and pathway analysis. This will establish current knowledge and identify key gaps in research. We show that the Haloferacaceae have significant genetic diversity between genera, with numerous gene gain and loss events in key genera. It also found that the model genus, Haloferax, has relatively low identified secondary metabolites compared to other genera within the family. Additionally, this study has identified potential biotechnology targets for heterologous expression in model organisms.

Keywords: Halobellus; Haloferax; Haloplanus; Archaea; Bioprospecting; Biosynthetic gene clusters; Biotechnology; Secondary metabolites.

Fig. 1

The number of amino acid substitutions per site from between sequences. Standard error estimate(s) are shown above the diagonal. Analyses were conducted using 100 Bootstrap replicates with the Poisson correction model. This analysis involved 7 amino acid sequences for the RpoB’ and PurA proteins across the Haloferacaceae and Enterobacteriaceae. All ambiguous positions were removed for each sequence pair (pairwise deletion option). There were a total of 1342 positions and 432 positions in the final dataset. Evolutionary analyses were conducted in MEGA11.

Fig. 2

Normalised average nucleotide identity of genera within the study. Genera were normalised by averaging values between all genera. *Denotes that several genomes had a value below 75% and no average value was calculated. Genera with only one species have no average value calculated across that genera and are left blank. A complete heatmap is provided as Supplementary Fig. 6.

Fig. 3

Haloferacaceae phylogenetic tree. The tree was constructed with PhyloPhlAn 3.0 then bootstrapped with IQ-TREE2 and visualised with iTOL^,,. Genera per current taxonomic classification with more than two genomes are represented in colour. T denotes type strain. An online interactive version is available at: https://itol.embl.de/shared/1PeDTZZoL0Jka.

Fig. 3

Haloferacaceae phylogenetic tree. The tree was constructed with PhyloPhlAn 3.0 then bootstrapped with IQ-TREE2 and visualised with iTOL^,,. Genera per current taxonomic classification with more than two genomes are represented in colour. T denotes type strain. An online interactive version is available at: https://itol.embl.de/shared/1PeDTZZoL0Jka.

Fig. 4

Phylogenetic tree of the Halobellus genus. This tree was based on core genes generated using IQ-TREE2 and panstripe with a bootstrap value of 100 and visualised with iTOL^,,. The tree shows total gene gain and loss rates indicated through a colour scale.

Fig. 5

Phylogenetic tree of the Haloferax genus. This tree was based on core genes generated using IQ-TREE2 and panstripe with a bootstrap value of 100 and visualised with iTOL^,,. The tree shows total gene gain and loss rates indicated through a colour scale.

Fig. 6

Phylogenetic tree of the Haloplanus genus. This tree was based on core genes generated using IQ-TREE2 and Panstripe with a bootstrap value of 100 and visualised with iTOL^,,. The tree shows total gene gain and loss rates indicated through a colour scale.

Fig. 7

A comparison of gene gain and loss events generated with Panstripe. This graph models between the Halobellus (red), Haloferax (blue) and Haloplanus (green) genera.

Fig. 8

Average KEGG annotation percentage across genera in the Haloferacaeae family.

Fig. 9

Average annotated metabolism genes across genera in the Haloferacaceae family.

Fig. 10

Normalized biosynthetic gene cluster (BGC) count across Haloferacaceae genera. BGC counts were normalized by dividing the total count of each BGC type present in a genus by the total genomes within that genus.