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

BMC Genomics

James S. Clegg¹  Tim De Meyer²  Louis Coussement²  Ziro Nambu³  Filip Van Nieuwerburgh⁴  Stephane Rombauts⁵  Yves Van de Peer⁶  Wannes Dermauw⁷  Thomas Van Leeuwen⁷  Marnik Vuylsteke⁸  Patrick Sorgeloos⁹  Gilbert Van Stappen⁹  Peter Bossier⁹  Stephanie De Vos^1,10  Parisa Norouzitallab^1,11 

[1] Coastal and Marine Sciences Institute, University of California, Bodega Bay, Davis, CA, USA;Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium;Department of Medical Technology, School of Health Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka, Japan;Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium;Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium;Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium;Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa;Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium;GNOMIXX, Boterbloemstraat 26, 9090, Melle, Belgium;Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium;Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium;Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium;Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium;Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium;

关键词: Arthropod;    Genome;    Transcriptome;    Assembly;    Annotation;    Extremophile;    Salinity;    Anoxia;    Artemia;    Brine shrimp;   

DOI  :  10.1186/s12864-021-07937-z

来源: Springer

【 摘 要 】

BackgroundBrine 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.Results and discussionHere, 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.ConclusionsA relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.

【 授权许可】

CC BY