Document of bibliographic reference 392836

BibliographicReference record

Type

Bibliographic resource

Type of document

Book/Monograph

Type of document

Dissertation

BibLvlCode

M

Title

Comparative genomic analysis of halophilic organisms

Abstract

Halophilic organisms thrive in environments with high NaCl content, displaying diverse metabolic strategies and adaptations. Research on halophiles has intensified in recent years as their adaptations, evolutionary history, and biotechnological potential are explored. In this PhD thesis, we first attempt to establish a database of these organisms and then analyze an extensive collection of representatives of the class Halobacteria (Archaea) in terms of their evolutionary relationships, amino acid profiles in their proteomes as well as their gene content. In particular, in a first stage, through an extensive literature search, over 1250 halophilic species from all three domains of life (Archaea, Bacteria, Eukaryotes) were recorded. These were organized in a database (HaloDom) along with a variety of metadata such as salinity range, habitat, taxonomic ranking, genomic data availability, etc., through an interface with user-friendly search functions. HaloDom is currently the most up-to-date and extensive online and freely available database of halophilic organisms and a useful repository for related research. In a second step, phylogenetic relationships in 124 Halobacteria and 33 outgroups were thoroughly investigated using 242 protein markers. The maximum likelihood phylogenetic tree obtained using the IQ-TREE program elucidates and updates previously problematic genealogical relationships of different groups of the Halobacteria clade. By examining amino acid profiles from Halobacteria, we confirmed previous findings and identified a distinct profile for previously known halophilic organisms. We observed similarities of profiles to non-halophilic species, suggesting possible convergent evolution or horizontal gene transfer. Also, different protein groups within Halobacteria were observed to show differences in their amino acid profiles. Taking advantage of the amino acid profile data, we developed HaloPredictor, a tool that detects salinity adaptations in protein sequences, which is available online. Finally, analyzing the Halobacteria pan-genome revealed an open pan-genome with several novel genes. Among 76 genomes, 814 core genes, 13752 accessory genes and 9010 cloud genes were identified for a total of 23576 gene clusters. An investigation of genes with multiple copies was performed, as well as functional annotation. This thesis provides valuable findings for future studies on metagenomics, medicine, and biotechnology, offering insights for further understanding of extremophiles and their better exploitation in industry.

Bibliographic citation

Loukas, A. (2014). Comparative genomic analysis of halophilic organisms. PhD Thesis. Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessalonik: Thessaloniki. 168 pp.

Topic

Marine

Access rights

open access

Is accessible for free

true