Genome Annotation and Comparative Analysis of Dunaliella Species Under Extreme Conditions

This study reports the first high-quality genome assembly of Dunaliella acidophila, a photosynthetic microalgae uniquely adapted to thrive in extremely acidic and metal rich environments. By leveraging Oxford Nanopore long read sequencing technology, a draft genome that captures the complexity of this extremophilic organism was assembled. Genome annotation was performed using a protein homology-based pipeline with MetaEuk, allowing for the prediction of protein-coding genes in the absence of transcriptomic evidence. This annotation strategy enabled the efficient identification of coding regions while avoiding biases introduced by condition specific expression data. To place the genome of D. acidophila in an evolutionary and functional context, comparative analyses were conducted with publicly available genomes from other Dunaliella species, as well as selected Chlamydomonas and Chlorella strains that represent a spectrum of ecological adaptations. Functional annotation of the predicted proteome was carried out using the eggNOG-mapper platform, which provided orthology-based functional assignments, Gene Ontology (GO) terms, and KEGG Orthology (KO) identifiers. In addition, orthologous gene clustering was performed using OrthoFinder to identify conserved gene sets and lineage-specific expansions potentially associated with acid resistance and environmental stress responses. Particularly, pseudo enrichment analyses of GO and KO terms revealed putative molecular pathways and gene functions that may underlie the unique capacity of D. acidophila to tolerate low pH conditions and the presence of heavy metals. These findings offer new insights into the adaptive mechanisms employed by this microalgae to maintain homeostasis and photosynthetic efficiency under extreme stress. Phylogenetic reconstruction based on core single-copy orthologs and ribosomal RNA genes strongly supported the placement of D. acidophila as an early diverging lineage within the Dunaliella genus. This positioning suggests a deep evolutionary divergence potentially linked to its adaptation to acidic environments, highlighting its value as a model organism for studying extremophilic photosynthetic eukaryotes.