Keilin D. The problem of anabiosis or latent life: history and current concept. Proc R Soc Lond B Biol Sci. 1959;150(939):149–91. https://doi.org/10.1098/rspb.1959.0013.
Article
CAS
PubMed
Google Scholar
Crowe J, Hoekstra F, Crowe L. Anhydrobiosis. Annu Rev Physiol. 1992;54(1):579–99. https://doi.org/10.1146/annurev.ph.54.030192.003051.
Article
CAS
PubMed
Google Scholar
Mobjerg N, Halberg KA, Jorgensen A, Persson D, Bjorn M, Ramlov H, et al. Survival in extreme environments - on the current knowledge of adaptations in tardigrades. Acta Physiol. 2011;202(3):409–20. https://doi.org/10.1111/j.1748-1716.2011.02252.x.
Article
CAS
Google Scholar
Hengherr S, Worland MR, Reuner A, Brummer F, Schill RO. High-temperature tolerance in anhydrobiotic tardigrades is limited by glass transition. Physiol Biochem Zool. 2009;82(6):749–55. https://doi.org/10.1086/605954.
Article
CAS
PubMed
Google Scholar
Hengherr S, Worland MR, Reuner A, Brummer F, Schill RO. Freeze tolerance, supercooling points and ice formation: comparative studies on the subzero temperature survival of limno-terrestrial tardigrades. J Exp Biol. 2009;212(Pt 6):802–7. https://doi.org/10.1242/jeb.025973.
Article
CAS
PubMed
Google Scholar
Jönsson KI, Rabbow E, Schill RO, Harms-Ringdahl M, Rettberg P. Tardigrades survive exposure to space in low earth orbit. Curr Biol. 2008;18(17):R729–31. https://doi.org/10.1016/j.cub.2008.06.048.
Article
CAS
PubMed
Google Scholar
Ono F, Mori Y, Takarabe K, Fujii A, Saigusa M, Matsushima Y, et al. Effect of ultra-high pressure on small animals, tardigrades and Artemia. Cogent Phys. 2016;3(1):1167575. https://doi.org/10.1080/23311940.2016.1167575.
Article
Google Scholar
Ramløv H, Westh P. Cryptobiosis in the Eutardigrade Adorybiotus (Richtersius) coronifer: tolerance to alcohols, temperature and de novo protein synthesis. Zool Anz. 2001;240(3–4):517–23. https://doi.org/10.1078/0044-5231-00062.
Article
Google Scholar
Horikawa DD, Cumbers J, Sakakibara I, Rogoff D, Leuko S, Harnoto R, et al. Analysis of DNA repair and protection in the tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation. PLoS One. 2013;8(6):e64793. https://doi.org/10.1371/journal.pone.0064793.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altiero T, Guidetti R, Caselli V, Cesari M, Rebecchi L. Ultraviolet radiation tolerance in hydrated and desiccated eutardigrades. J Zool Syst Evol Res. 2011;49(s1):104–10. https://doi.org/10.1111/j.1439-0469.2010.00607.x.
Article
Google Scholar
Jonsson KI, Hygum TL, Andersen KN, Clausen LK, Mobjerg N. Tolerance to gamma radiation in the marine Heterotardigrade, Echiniscoides sigismundi. PLoS One. 2016;11(12):e0168884. https://doi.org/10.1371/journal.pone.0168884.
Article
CAS
PubMed
PubMed Central
Google Scholar
Honda Y, Tanaka M, Honda S. Trehalose extends longevity in the nematode Caenorhabditis elegans. Aging Cell. 2010;9(4):558–69. https://doi.org/10.1111/j.1474-9726.2010.00582.x.
Article
CAS
PubMed
Google Scholar
Moore DS, Hansen R, Hand SC. Liposomes with diverse compositions are protected during desiccation by LEA proteins from Artemia franciscana and trehalose. Biochim Biophys Acta. 2016;1858(1):104–15. https://doi.org/10.1016/j.bbamem.2015.10.019.
Article
CAS
PubMed
Google Scholar
Sakurai M, Furuki T, Akao K, Tanaka D, Nakahara Y, Kikawada T, et al. Vitrification is essential for anhydrobiosis in an African chironomid, Polypedilum vanderplanki. Proc Natl Acad Sci U S A. 2008;105(13):5093–8. https://doi.org/10.1073/pnas.0706197105.
Article
PubMed
PubMed Central
Google Scholar
Crowe J, Clegg J, Crowe L. Anhydrobiosis: the water replacement hypothesis. Boston: Springer; 1998.
Google Scholar
Caramelo JJ, Iusem ND. When cells lose water: lessons from biophysics and molecular biology. Prog Biophys Mol Biol. 2009;99(1):1–6. https://doi.org/10.1016/j.pbiomolbio.2008.10.001.
Article
CAS
PubMed
Google Scholar
Goyal K, Tisi L, Basran A, Browne J, Burnell A, Zurdo J, et al. Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein. J Biol Chem. 2003;278(15):12977–84. https://doi.org/10.1074/jbc.M212007200.
Article
CAS
PubMed
Google Scholar
Goldgur Y, Rom S, Ghirlando R, Shkolnik D, Shadrin N, Konrad Z, et al. Desiccation and zinc binding induce transition of tomato abscisic acid stress ripening 1, a water stress- and salt stress-regulated plant-specific protein, from unfolded to folded state. Plant Physiol. 2007;143(2):617–28. https://doi.org/10.1104/pp.106.092965.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oliveira E, Amara I, Bellido D, Odena MA, Dominguez E, Pages M, et al. LC-MSMS identification of Arabidopsis thaliana heat-stable seed proteins: enriching for LEA-type proteins by acid treatment. J Mass Spectrom. 2007;42(11):1485–95. https://doi.org/10.1002/jms.1292.
Article
CAS
PubMed
Google Scholar
Hand SC, Menze MA, Toner M, Boswell L, Moore D. LEA proteins during water stress: not just for plants anymore. Annu Rev Physiol. 2011;73(1):115–34. https://doi.org/10.1146/annurev-physiol-012110-142203.
Article
CAS
PubMed
Google Scholar
Hengherr S, Heyer AG, Kohler HR, Schill RO. Trehalose and anhydrobiosis in tardigrades—evidence for divergence in responses to dehydration. FEBS J. 2008;275(2):281–8. https://doi.org/10.1111/j.1742-4658.2007.06198.x.
Article
CAS
PubMed
Google Scholar
Jönsson KI, Persson O. Trehalose in three species of desiccation tolerant tardigrades. Open Zool J. 2010;3(1):1–5. https://doi.org/10.2174/1874336601003010001.
Article
CAS
Google Scholar
Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, et al. Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS Biol. 2017;15(7):e2002266. https://doi.org/10.1371/journal.pbio.2002266.
Article
CAS
PubMed
PubMed Central
Google Scholar
Förster F, Liang C, Shkumatov A, Beisser D, Engelmann JC, Schnolzer M, et al. Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. BMC Genomics. 2009;10(469):1–10. https://doi.org/10.1186/1471-2164-10-469.
Article
CAS
Google Scholar
Kamilari M, Jorgensen A, Schiott M, Mobjerg N. Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages. BMC Genomics. 2019;20(1):607. https://doi.org/10.1186/s12864-019-5912-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tunnacliffe A, Lapinski J. Resurrecting Van Leeuwenhoek's rotifers: a reappraisal of the role of disaccharides in anhydrobiosis. Philos Trans R Soc Lond Ser B Biol Sci. 2003;358(1438):1755–71. https://doi.org/10.1098/rstb.2002.1214.
Article
CAS
Google Scholar
Campos F, Cuevas-Velazquez C, Fares MA, Reyes JL, Covarrubias AA. Group 1 LEA proteins, an ancestral plant protein group, are also present in other eukaryotes, and in the archeae and bacteria domains. Mol Gen Genomics. 2013;288(10):503–17. https://doi.org/10.1007/s00438-013-0768-2.
Article
CAS
Google Scholar
Hibshman JD, Clegg JS, Goldstein B. Mechanisms of desiccation tolerance: themes and variations in brine shrimp, roundworms, and tardigrades. Front Physiol. 2020;11:592016. https://doi.org/10.3389/fphys.2020.592016.
Article
PubMed
PubMed Central
Google Scholar
Hashimoto T, Horikawa D, Saito Y, Kuwahara H, Kozuka-Hata H, Shin I, et al. Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nat Commun. 2016;7(1):12808. https://doi.org/10.1038/ncomms12808.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamaguchi A, Tanaka S, Yamaguchi S, Kuwahara H, Takamura C, Imajoh-Ohmi S, et al. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade. PLoS One. 2012;7(8):e44209. https://doi.org/10.1371/journal.pone.0044209.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tanaka S, Tanaka J, Miwa Y, Horikawa DD, Katayama T, Arakawa K, et al. Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic tardigrade improve osmotic tolerance of human cells. PLoS One. 2015;10(2):e0118272. https://doi.org/10.1371/journal.pone.0118272.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bemm F, Burleigh L, Foerster F, Schmucki R, Ebeling M, Janzen C, et al. Draft genome of the Eutardigrade Milnesium tardigradum sheds light on ecdysozoan evolution. bioRxiv. 2017; preprint first posted online.
Kondo K, Kubo T, Kunieda T. Suggested involvement of PP1/PP2A activity and De novo gene expression in Anhydrobiotic survival in a tardigrade, Hypsibius dujardini, by chemical genetic approach. PLoS One. 2015;10(12):e0144803. https://doi.org/10.1371/journal.pone.0144803.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watanabe M, Kikawada T, Minagawa N, Yukuhiro F, Okuda T. Mechanism allowing an insect to survive complete dehydration and extreme temperatures. J Exp Biol. 2002;205(Pt 18):2799–802. https://doi.org/10.1242/jeb.205.18.2799.
Article
CAS
PubMed
Google Scholar
Erkut C, Vasilj A, Boland S, Habermann B, Shevchenko A, Kurzchalia TV. Molecular strategies of the Caenorhabditis elegans dauer larva to survive extreme desiccation. PLoS One. 2013;8(12):e82473. https://doi.org/10.1371/journal.pone.0082473.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wright JC. Desiccation tolerance and water-retentive mechanisms in tardigrades. J Exp Biol. 1989;142(1):267–92. https://doi.org/10.1242/jeb.142.1.267.
Article
Google Scholar
Persson D, Halberg KA, Jorgensen A, Ricci C, Mobjerg N, Kristensen RM. Extreme stress tolerance in tardigrades: surviving space conditions in low earth orbit. J Zool Syst Evol Res. 2011;49(s1):90–7. https://doi.org/10.1111/j.1439-0469.2010.00605.x.
Article
Google Scholar
Heidemann NWT, Smith DK, Hygum TL, Stapane L, Clausen LKB, Jørgensen A, et al. Osmotic stress tolerance in semi-terrestrial tardigrades. Zool J Linnean Soc. 2016;178(4):912–8. https://doi.org/10.1111/zoj.12502.
Article
Google Scholar
Hygum TL, Fobian D, Kamilari M, Jorgensen A, Schiott M, Grosell M, et al. Comparative investigation of copper tolerance and identification of putative tolerance related genes in tardigrades. Front Physiol. 2017;8:95. https://doi.org/10.3389/fphys.2017.00095.
Article
PubMed
PubMed Central
Google Scholar
Jorgensen A, Faurby S, Hansen JG, Mobjerg N, Kristensen RM. Molecular phylogeny of Arthrotardigrada (Tardigrada). Mol Phylogenet Evol. 2010;54(3):1006–15. https://doi.org/10.1016/j.ympev.2009.10.006.
Article
PubMed
Google Scholar
Arakawa K. No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A. 2016;113(22):E3057. https://doi.org/10.1073/pnas.1602711113.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arakawa K, Yoshida Y, Tomita M. Genome sequencing of a single tardigrade Hypsibius dujardini individual. Sci Data. 2016;3(1):160063. https://doi.org/10.1038/sdata.2016.63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoshida Y, Konno S, Nishino R, Murai Y, Tomita M, Arakawa K. Ultralow input genome sequencing library preparation from a single tardigrade specimen. J Vis Exp. 2018;137(137). https://doi.org/10.3791/57615.
Laetsch D, Blaxter M. BlobTools: Interrogation of genome assemblies [version 1; referees: 2 approved with reservations]. F1000Research. 2017;6:1287.
Article
Google Scholar
Stec D, Krzywanski L, Arakawa K, Michalczyk L. A new redescription of Richtersius coronifer, supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus Richtersius (Eutardigrada). Zool Lett. 2020;6(1):2. https://doi.org/10.1186/s40851-020-0154-y.
Article
Google Scholar
Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, et al. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A. 2016;113(18):5053–8. https://doi.org/10.1073/pnas.1600338113.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cornette R, Kikawada T. The induction of anhydrobiosis in the sleeping chironomid: current status of our knowledge. IUBMB Life. 2011;63(6):419–29. https://doi.org/10.1002/iub.463.
Article
CAS
PubMed
Google Scholar
Evangelista CCS, Guidelli GV, Borges G, Araujo TF, Souza TAJ, Neves U, et al. Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus. Genet Mol Biol. 2017;40(4):790–802. https://doi.org/10.1590/1678-4685-gmb-2017-0030.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rytkonen KT, Williams TA, Renshaw GM, Primmer CR, Nikinmaa M. Molecular evolution of the metazoan PHD-HIF oxygen-sensing system. Mol Biol Evol. 2011;28(6):1913–26. https://doi.org/10.1093/molbev/msr012.
Article
CAS
PubMed
Google Scholar
Graham AM, Barreto FS. Loss of the HIF pathway in a widely distributed intertidal crustacean, the copepod Tigriopus californicus. Proc Natl Acad Sci U S A. 2019;116(26):12913–8. https://doi.org/10.1073/pnas.1819874116.
Article
CAS
PubMed
PubMed Central
Google Scholar
Battaglia M, Covarrubias AA. Late Embryogenesis Abundant (LEA) proteins in legumes. Front Plant Sci. 2013;4:190. https://doi.org/10.3389/fpls.2013.00190.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sasaki K, Christov NK, Tsuda S, Imai R. Identification of a novel LEA protein involved in freezing tolerance in wheat. Plant Cell Physiol. 2014;55(1):136–47. https://doi.org/10.1093/pcp/pct164.
Article
CAS
PubMed
Google Scholar
Piszkiewicz S, Gunn KH, Warmuth O, Propst A, Mehta A, Nguyen KH, et al. Protecting activity of desiccated enzymes. Protein Sci. 2019;28(5):941–51. https://doi.org/10.1002/pro.3604.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnson CG. The maintenance of high atmospheric humidities for entomological work with glycerol-water mixtures. Ann Appl Biol. 1940;27(2):295–9. https://doi.org/10.1111/j.1744-7348.1940.tb07499.x.
Article
CAS
Google Scholar
Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. 2010. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017;33(14):2202–4. https://doi.org/10.1093/bioinformatics/btx153.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29(21):2669–77. https://doi.org/10.1093/bioinformatics/btt476.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jo H, Koh G. Faster single-end alignment generation utilizing multi-thread for BWA. Biomed Mater Eng. 2015;26(Suppl 1):S1791–6. https://doi.org/10.3233/BME-151480.
Article
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. Genome project data processing subgroup: the sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402. https://doi.org/10.1093/nar/25.17.3389.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35(Database issue):D61–5. https://doi.org/10.1093/nar/gkl842.
Article
CAS
PubMed
Google Scholar
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2. https://doi.org/10.1093/bioinformatics/btv351.
Article
CAS
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. https://doi.org/10.1186/gb-2013-14-4-r36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics. 2016;32(5):767–9. https://doi.org/10.1093/bioinformatics/btv661.
Article
CAS
PubMed
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52. https://doi.org/10.1038/nbt.1883.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bairoch A, Boeckmann B, Ferro S, Gasteiger E. Swiss-Prot: juggling between evolution and stability. Brief Bioinform. 2004;5(1):39–55. https://doi.org/10.1093/bib/5.1.39.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30. https://doi.org/10.1093/nar/28.1.27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35(Web Server issue):182–5.
Article
Google Scholar
Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(Suppl 1):i351–8. https://doi.org/10.1093/bioinformatics/bti1018.
Article
CAS
PubMed
Google Scholar
Smit A, Hubley R, Green P: RepeatMasker Open-4.0. http://www.repeatmasker.org. 2013–2015.
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64. https://doi.org/10.1093/nar/25.5.955.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–8. https://doi.org/10.1093/nar/gkm160.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bray N, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34(5):525–7. https://doi.org/10.1038/nbt.3519.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https://doi.org/10.1186/s13059-014-0550-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059–66. https://doi.org/10.1093/nar/gkf436.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50. https://doi.org/10.1093/molbev/msp077.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23(1):127–8. https://doi.org/10.1093/bioinformatics/btl529.
Article
CAS
PubMed
Google Scholar
Perkins DN, Pappin DJC, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999;20(18):3551–67. https://doi.org/10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2.
Article
CAS
PubMed
Google Scholar
Prilusky J, Felder C, Zeev-Ben-Mordehai T, Rydberg E, Man O, Beckmann J, et al. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics. 2005;21(16):3435–8. https://doi.org/10.1093/bioinformatics/bti537.
Article
CAS
PubMed
Google Scholar
Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics. 2004;20(13):2138–9. https://doi.org/10.1093/bioinformatics/bth195.
Article
CAS
PubMed
Google Scholar