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

Stephanie De Vos (UGent) , Stephane Rombauts (UGent) , Louis Coussement (UGent) , Wannes Dermauw (UGent) , Marnik Vuylsteke (UGent) , Patrick Sorgeloos (UGent) , James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh (UGent) , Parisa Norouzitallab (UGent) , et al.
(2021) BMC GENOMICS. 22(1).
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Abstract
Background: 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. Results and discussion: 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. Conclusions: 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.
Keywords
Annotation, Anoxia, Artemia, Arthropod, Assembly, Brine shrimp, Extremophile, Genome, Salinity, Transcriptome, BRINE SHRIMP, DESICCATION TOLERANCE, ANIMAL EXTREMOPHILE, EXPRESSION ANALYSIS, PHOSPHOLIPASE-D, LEA PROTEINS, SALT STRESS, FRANCISCANA, EMBRYOS, GENE

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Citation

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MLA
De Vos, Stephanie, et al. “The Genome of the Extremophile Artemia Provides Insight into Strategies to Cope with Extreme Environments.” BMC GENOMICS, vol. 22, no. 1, 2021, doi:10.1186/s12864-021-07937-z.
APA
De Vos, S., Rombauts, S., Coussement, L., Dermauw, W., Vuylsteke, M., Sorgeloos, P., … Bossier, P. (2021). The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments. BMC GENOMICS, 22(1). https://doi.org/10.1186/s12864-021-07937-z
Chicago author-date
De Vos, Stephanie, Stephane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, et al. 2021. “The Genome of the Extremophile Artemia Provides Insight into Strategies to Cope with Extreme Environments.” BMC GENOMICS 22 (1). https://doi.org/10.1186/s12864-021-07937-z.
Chicago author-date (all authors)
De Vos, Stephanie, Stephane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer, and Peter Bossier. 2021. “The Genome of the Extremophile Artemia Provides Insight into Strategies to Cope with Extreme Environments.” BMC GENOMICS 22 (1). doi:10.1186/s12864-021-07937-z.
Vancouver
1.
De Vos S, Rombauts S, Coussement L, Dermauw W, Vuylsteke M, Sorgeloos P, et al. The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments. BMC GENOMICS. 2021;22(1).
IEEE
[1]
S. De Vos et al., “The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments,” BMC GENOMICS, vol. 22, no. 1, 2021.
@article{8721801,
  abstract     = {{Background: 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.

Results and discussion: 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.

Conclusions: 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.}},
  articleno    = {{635}},
  author       = {{De Vos, Stephanie and Rombauts, Stephane and Coussement, Louis and Dermauw, Wannes and Vuylsteke, Marnik and Sorgeloos, Patrick and Clegg, James S. and Nambu, Ziro and Van Nieuwerburgh, Filip and Norouzitallab, Parisa and Van Leeuwen, Thomas and De Meyer, Tim and Van Stappen, Gilbert and Van de Peer, Yves and Bossier, Peter}},
  issn         = {{1471-2164}},
  journal      = {{BMC GENOMICS}},
  keywords     = {{Annotation,Anoxia,Artemia,Arthropod,Assembly,Brine shrimp,Extremophile,Genome,Salinity,Transcriptome,BRINE SHRIMP,DESICCATION TOLERANCE,ANIMAL EXTREMOPHILE,EXPRESSION ANALYSIS,PHOSPHOLIPASE-D,LEA PROTEINS,SALT STRESS,FRANCISCANA,EMBRYOS,GENE}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{26}},
  title        = {{The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments}},
  url          = {{http://doi.org/10.1186/s12864-021-07937-z}},
  volume       = {{22}},
  year         = {{2021}},
}
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