The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

• Published in: BMC genomics Vol. 22; no. 1; pp. 635 - 26
• Main Authors: De Vos, Stephanie, Rombauts, Stephane, Coussement, Louis, Dermauw, Wannes, Vuylsteke, Marnik, Sorgeloos, Patrick, Clegg, James S, Nambu, Ziro, Van Nieuwerburgh, Filip, Norouzitallab, Parisa, Van Leeuwen, Thomas, De Meyer, Tim, Van Stappen, Gilbert, Van de Peer, Yves, Bossier, Peter
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 31.08.2021; BioMed Central; BMC
• Subjects: Animals; Annotation; Anoxia; Artemia; Artemia - genetics; Arthropod; Arthropods; Assembly; Autophagy; Cell cycle; Cellular stress response; Control; Crustaceans; Cysts; D gene; Embryogenesis; Embryonic growth stage; Endocytosis; Enzymes; Exocytosis; Extreme Environments; Extremophile; Extremophiles; Gene expression; Genes; Genetic aspects; Genome; Genomes; Genomics; Heat shock proteins; Hypoxia (Aquatic ecology); Identification and classification; Inbreeding; Ion transport; Management; Measurement; Metabolism; Microorganisms; Mitochondria; Oxidative stress; Phagocytosis; Phospholipase D; Plant stress; Prevention; Proteins; Salinity; Salinity effects; Shrimp culture; Signal transduction; Taxonomy; TOR protein; Transcriptome; Trehalose; South Africa; Anoxia; Transcriptome; Arthropod; Brine shrimp; Artemia; Genome; Extremophile; Annotation; Assembly; Salinity
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-021-07937-z

Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors. Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions. A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.