Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature [Internet]. 2001;409(6818):363–6. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11201747
Denli AM, Hannon GJ. RNAi: an ever-growing puzzle. Trends Biochem Sci [Internet]. 2003;28(4):196–201. Available from: https://www.sciencedirect.com/science/article/pii/S0968000403000586
Sidahmed A, Abdalla S, Mahmud S, Wilkie B. Antiviral innate immune response of RNA interference. The Journal of Infection in Developing Countries [Internet]. 2014;8(07):804–10. Available from: https://jidc.org/index.php/journal/article/view/25022288
Heigwer F, Port F, Boutros M. RNA Interference (RNAi) Screening in Drosophila. Genetics [Internet]. 2018;208(3):853–74. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844339/
Shabalina SA, Koonin EV. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol [Internet]. 2008;23(10):578–87. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695246/
Ding SW, Han Q, Wang J, Li WX. Antiviral RNA interference in mammals. Curr Opin Immunol [Internet]. 2018;54:109–14. Available from: https://www.sciencedirect.com/science/article/pii/S0952791518300803
de Jong D, Eitel M, Jakob W, Osigus HJ, Hadrys H, DeSalle R, et al. Multiple dicer genes in the early-diverging Metazoa. Mol Biol Evol. 2009;26(6):1333–40. https://doi.org/10.1093/molbev/msp042.
Zapletal D, Kubicek K, Svoboda P, Stefl R. Dicer structure and function: conserved and evolving features. EMBO Rep [Internet]. 2023;24(7):e57215. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10328071/
Welker NC, Maity TS, Ye X, Aruscavage PJ, Krauchuk AA, Liu Q et al. Dicer’s helicase domain discriminates dsRNA termini to promote an altered reaction mode. Mol Cell [Internet]. 2011;41(5):589–99. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061311/
Sinha NK, Trettin KD, Aruscavage PJ, Bass BL. Drosophila Dicer-2 cleavage is mediated by helicase- and dsRNA termini-dependent states that are modulated by Loquacious-PD. Mol Cell [Internet]. 2015;58(3):406–17. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4433149/
MacKay CR, Wang JP, Kurt-Jones EA. Dicer’s role as an antiviral: still an enigma. Curr Opin Immunol [Internet]. 2014;0:49–55. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932008/
Ciechanowska K, Pokornowska M, Kurzyńska-Kokorniak A. Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases. Int J Mol Sci [Internet]. 2021;22(2):616. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7827160/
Hansen SR, Aderounmu AM, Donelick HM, Bass BL. Dicer’s Helicase Domain: A Meeting Place for Regulatory Proteins. Cold Spring Harb Symp Quant Biol [Internet]. 2019;84:185–93. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384945/
Ma E, MacRae IJ, Kirsch JF, Doudna JA. Auto-inhibition of Human Dicer by its Internal Helicase Domain. J Mol Biol [Internet]. 2008;380(1):237–43. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927216/
Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature [Internet]. 2008;455(7217):1193–7. Available from: https://www.nature.com/articles/nature07415
Mukherjee K, Campos H, Kolaczkowski B. Evolution of Animal and Plant Dicers: Early Parallel Duplications and Recurrent Adaptation of Antiviral RNA Binding in Plants. Mol Biol Evol [Internet]. 2013;30(3):627–41. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563972/
Jia H, Kolaczkowski O, Rolland J, Kolaczkowski B. Increased affinity for RNA targets evolved early in animal and plant dicer lineages through different structural mechanisms. Mol Biol Evol. 2017;34(12):3047–63. https://doi.org/10.1093/molbev/msx187.
Formaggioni A, Cavalli G, Hamada M, Sakamoto T, Plazzi F, Passamonti M. The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa. Genome Biol Evol [Internet]. 2024;16(5):1–18. Available from: https://doi.org/10.1093/gbe/evae098
Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell [Internet]. 2004;117(1):69–81. Available from: http://www.ncbi.nlm.nih.gov/pubmed/15066283
Mapalo MA, Wolfe JM, Ortega-Hernández J. Cretaceous amber inclusions illuminate the evolutionary origin of tardigrades. Commun Biol. 2024;7(1):953. https://doi.org/10.1038/s42003-024-06643-2.
Giacomelli M, Vecchi M, Guidetti R, Rebecchi L, Donoghue PCJ, Lozano-Fernandez J et al. CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora. Lanfear R, editor. Genome Biol Evol [Internet]. 2025;17(1):1–14. Available from: https://doi.org/10.1093/gbe/evae273
Laumer CE, Fernández R, Lemer S, Combosch D, Kocot KM, Riesgo A, et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc Biol Sci. 2019;286(1906):20190831. https://doi.org/10.1098/rspb.2019.0831.
Schokraie E, Hotz-Wagenblatt A, Warnken U, Frohme M, Dandekar T, Schill RO, et al. Investigating heat shock proteins of tardigrades in active versus anhydrobiotic state using shotgun proteomics. J Zool Syst Evol Res. 2011;49(s1):111–9. https://doi.org/10.1111/j.1439-0469.2010.00608.x.
Nelson DR, Bartels PJ, Guil N. Tardigrade Ecology. In: Schill RO, editor. Water Bears: The Biology of Tardigrades [Internet]. Cham: Springer International Publishing; 2018. pp. 163–210. Available from: https://doi.org/10.1007/978-3-319-95702-9_7
Buda J, Olszanowski Z, Wierzgoń M, Zawierucha K. Tardigrades and oribatid mites in bryophytes from geothermally active lava fields (Krafla, Iceland) and the description of Pilatobius islandicus sp. nov. (Eutardigrada) [Internet]. 2018. Available from: https://rebus.us.edu.pl/handle/20.500.12128/7700
Romano IIIF, Gallo M, D’Addabbo R, Accogli G, Baguley J, Montagna P. Deep-sea tardigrades in the northern Gulf of Mexico with a description of a new species of Coronarctidae (Tardigrada: Arthrotardigrada), Coronarctus mexicus. Journal of Zoological Systematics and Evolutionary Research [Internet]. 2011;49(s1):48–52. Available from: https://onlinelibrary.wiley.com/doi/abs/https://doi.org/10.1111/j.1439-0469.2010.00597.x
Tenlen JR, McCaskill S, Goldstein B. RNA interference can be used to disrupt gene function in tardigrades. Dev Genes Evol [Internet]. 2013;223(3):171–81. Available from: http://www.ncbi.nlm.nih.gov/pubmed/23187800
Giovannini I, Boothby TC, Cesari M, Goldstein B, Guidetti R, Rebecchi L. Production of reactive oxygen species and involvement of bioprotectants during anhydrobiosis in the tardigrade Paramacrobiotus spatialis. Sci Rep [Internet]. 2022;12(1):1938. Available from: https://www.nature.com/articles/s41598-022-05734-6
Schill RO, Steinbrück G. Identification and differentiation of heterotardigrada and eutardigrada species by riboprinting. J Zool Syst Evol Res. 2007;45(3):184–90. https://doi.org/10.1111/j.1439-0469.2007.00409.x.
Møbjerg N, Jørgensen A, Kristensen RM, Neves RC. Morphology and Functional Anatomy. In: Schill RO, editor. Water Bears: The Biology of Tardigrades [Internet]. Cham: Springer International Publishing; 2018. pp. 57–94. Available from: https://doi.org/10.1007/978-3-319-95702-9_2
Kamilari M, Jørgensen A, Schiøtt M, Møbjerg N. Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages. BMC Genomics. 2019;20(1):607.
Stec D, Krzywański Ł, Arakawa K, Michalczyk Ł. 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.
Boothby TC, Tapia H, Brozena AH, Piszkiewicz S, Smith AE, Giovannini I et al. Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Mol Cell [Internet]. 2017;65(6):975–984.e5. Available from: https://doi.org/10.1016/j.molcel.2017.02.018
Anoud M, Delagoutte E, Helleu Q, Brion A, Duvernois-Berthet E, As M et al. Comparative transcriptomics reveal a novel tardigrade-specific DNA-binding protein induced in response to ionizing radiation. Elife [Internet]. 2024;13:1–29. Available from: https://elifesciences.org/articles/92621
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.
Mapalo MA, Arakawa K, Baker CM, Persson DK, Mirano-Bascos D, Giribet G. The unique antimicrobial recognition and signaling pathways in tardigrades with a comparison across ecdysozoa. G3 Genes|Genomes|Genetics. 2020;10(3):1137–48.
Murai Y, Yagi-Utsumi M, Fujiwara M, Tanaka S, Tomita M, Kato K et al. Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada. BMC Genomics [Internet]. 2021;22(1):813. Available from: http://biorxiv.org/content/early/2020/10/28/2020.10.27.358333.abstract
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.
Criscuolo A, Gribaldo S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 2010;10(1):210. https://doi.org/10.1186/1471-2148-10-210.
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-tree 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530–4. https://doi.org/10.1093/molbev/msaa015.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods [Internet]. 2017;14(6):587–9. Available from: https://www.nature.com/articles/nmeth.4285
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307–21. https://doi.org/10.1093/sysbio/syq010.
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFboot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518–22. https://doi.org/10.1093/molbev/msx281.
Lartillot N, Rodrigue N, Stubbs D, Richer J, PhyloBayes MPI. Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment. Syst Biol [Internet]. 2013;62(4):611–5. Available from: https://doi.org/10.1093/sysbio/syt022
Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Kelley J, editor. Mol Biol Evol [Internet]. 2021;38(10):4647–54. Available from: https://academic.oup.com/mbe/article/38/10/4647/6329644
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods [Internet]. 2015;12(1):59–60. Available from: https://www.nature.com/articles/nmeth.3176
Herranz M, Stiller J, Worsaae K, Sørensen MV. Phylogenomic analyses of mud dragons (Kinorhyncha). Mol Phylogenet Evol [Internet]. 2022;168(December 2021):107375. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1055790321003080
Sato S, Cunha TJ, de Medeiros BAS, Khost DE, Sackton TB, Giribet G. Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi. Vieira C, editor. Genome Biol Evol [Internet]. 2023;15(3):1–6. Available from: https://doi.org/10.1093/gbe/evad021
Lord A, Cunha TJ, de Medeiros BAS, Sato S, Khost DE, Sackton TB et al. Expanding on Our Knowledge of Ecdysozoan Genomes: A Contiguous Assembly of the Meiofaunal Priapulan Tubiluchus corallicola. Wheat C, editor. Genome Biol Evol [Internet]. 2023;15(6):1–6. Available from: https://doi.org/10.1093/gbe/evad103
Wang HC, Minh BQ, Susko E, Roger AJ. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst Biol. 2018;67(2):216–35. https://doi.org/10.1093/sysbio/syx068.
Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res [Internet]. 2020;48(D1):D265–8. Available from: https://doi.org/10.1093/nar/gkz991
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nat Methods [Internet]. 2022;19(6):679–82. Available from: https://www.nature.com/articles/s41592-022-01488-1
Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V et al. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res [Internet]. 2021;49(W1):W431–7. Available from: https://academic.oup.com/nar/article/49/W1/W431/6270780
Grant BJ, Rodrigues APC, ElSawy KM, McCammon JA, Caves LSD. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics [Internet]. 2006;22(21):2695–6. Available from: https://academic.oup.com/bioinformatics/article/22/21/2695/252414
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res [Internet]. 2004;32(5):1792–7. Available from: http://www.ncbi.nlm.nih.gov/pubmed/15034147
Yoshida Y, Sugiura K, Tomita M, Matsumoto M, Arakawa K. Comparison of the transcriptomes of two tardigrades with different hatching coordination. BMC Dev Biol. 2019;19(1):1–9.
Krueger F, Babraham Institute. 2015. Trim Galore! A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. Available from: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635.
Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res [Internet]. 2020;9:ISCB Comm J-304. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222033/
Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014. https://doi.org/10.1093/bioinformatics/btt656.
Horton NJ, Kleinman K, Using. R and RStudio for Data Management, Statistical Analysis, and Graphics [Internet]. CRC Press; 2015. 280 p. Available from: https://books.google.com/books?id=W1G3BgAAQBAJ
Vergani-Junior CA, Tonon-da-Silva G, Inan MD, Mori MA. DICER: structure, function, and regulation. Biophys Rev. 2021;13(6):1081–90. https://doi.org/10.1007/s12551-021-00902-w.
Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ et al. Distinct Roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA Silencing Pathways. Cell [Internet]. 2004;117(1):69–81. Available from: https://www.cell.com/cell/abstract/S0092-8674(04)00261-2
Kidwell MA, Chan JM, Doudna JA. Evolutionarily Conserved Roles of the Dicer Helicase Domain in Regulating RNA Interference Processing. Journal of Biological Chemistry [Internet]. 2014;289(41):28352–62. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4192488/
Kaufman EJ, Miska EA. The microRNAs of Caenorhabditis elegans. Semin Cell Dev Biol [Internet]. 2010;21(7):728–37. Available from: https://www.sciencedirect.com/science/article/pii/S1084952110001060
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 2003;17(8):991–1008. https://doi.org/10.1101/gad.1074403.
Bukhari SIA, Vasquez-Rifo A, Gagné D, Paquet ER, Zetka M, Robert C et al. The microRNA pathway controls germ cell proliferation and differentiation in C. elegans. Cell Res [Internet]. 2012;22(6):1034–45. Available from: https://www.nature.com/articles/cr201231
McMenamin AJ, Daughenbaugh KF, Flenniken ML. The Heat Shock Response in the Western Honey Bee (Apis mellifera) is Antiviral. Viruses [Internet]. 2020;12(2):245. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077298/
Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL. Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. Elife [Internet]. 2023;12:e85120. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10159624/