1.Pucciarelli, S. et al. Molecular cold-adaptation of protein function and gene regulation: the case for comparative genomic analyses in marine ciliated protozoa. Mar Genomics 2, 57–66. https://doi.org/10.1016/j.margen.2009.03.008 (2009).Article
PubMed
Google Scholar
2.Pucciarelli, S., Marziale, F., Di Giuseppe, G., Barchetta, S. & Miceli, C. Ribosomal cold-adaptation: characterization of the genes encoding the acidic ribosomal P0 and P2 proteins from the Antarctic ciliate Euplotes focardii. Gene 360, 103–110. https://doi.org/10.1016/j.gene.2005.06.007 (2005).CAS
Article
PubMed
Google Scholar
3.Pucciarelli, S. & Miceli, C. Characterization of the cold-adapted alpha-tubulin from the psychrophilic ciliate Euplotes focardii. Extremophiles 6, 385–389. https://doi.org/10.1007/s00792-002-0268-5 (2002).CAS
Article
PubMed
Google Scholar
4.Yang, G. et al. Characterization and comparative analysis of psychrophilic and mesophilic alpha-amylases from Euplotes species: a contribution to the understanding of enzyme thermal adaptation. Biochem Biophys Res Commun 438, 715–720. https://doi.org/10.1016/j.bbrc.2013.07.113 (2013).CAS
Article
PubMed
Google Scholar
5.Prescott, D. M. The DNA of ciliated protozoa. Microbiol Rev 58, 233–267 (1994).CAS
Article
Google Scholar
6.Mollenbeck, M. & Klobutcher, L. A. De novo telomere addition to spacer sequences prior to their developmental degradation in Euplotes crassus. Nucleic Acids Res 30, 523–531 (2002).Article
Google Scholar
7.Swart, E. C. et al. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 11, e1001473. https://doi.org/10.1371/journal.pbio.1001473 (2013).CAS
Article
PubMed
PubMed Central
Google Scholar
8.Heyse, G., Jonsson, F., Chang, W. J. & Lipps, H. J. RNA-dependent control of gene amplification. Proc Natl Acad Sci U S A 107, 22134–22139. https://doi.org/10.1073/pnas.1009284107 (2010).ADS
Article
PubMed
PubMed Central
Google Scholar
9.Nowacki, M., Haye, J. E., Fang, W., Vijayan, V. & Landweber, L. F. RNA-mediated epigenetic regulation of DNA copy number. Proc Natl Acad Sci U S A 107, 22140–22144. https://doi.org/10.1073/pnas.1012236107 (2010).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
10.Dayeh, V. R. et al. Comparing a ciliate and a fish cell line for their sensitivity to several classes of toxicants by the novel application of multiwell filter plates to Tetrahymena. Res Microbiol 156, 93–103. https://doi.org/10.1016/j.resmic.2004.08.005 (2005).ADS
CAS
Article
PubMed
Google Scholar
11.Detrich, H. W., 3rd, Parker, S. K., Williams, R. C., Jr., Nogales, E. & Downing, K. H. Cold adaptation of microtubule assembly and dynamics. Structural interpretation of primary sequence changes present in the alpha- and beta-tubulins of Antarctic fishes. J Biol Chem 275, 37038–37047. https://doi.org/10.1074/jbc.M005699200 (2000).12.Manka, S. W. & Moores, C. A. Microtubule structure by cryo-EM: snapshots of dynamic instability. Essays Biochem 62, 737–751. https://doi.org/10.1042/EBC20180031 (2018).Article
PubMed
PubMed Central
Google Scholar
13.Inclan, Y. F. & Nogales, E. Structural models for the self-assembly and microtubule interactions of gamma-, delta- and epsilon-tubulin. J Cell Sci 114, 413–422 (2001).CAS
Article
Google Scholar
14.Chiappori, F. et al. Structural thermal adaptation of beta-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii. Proteins 80, 1154–1166. https://doi.org/10.1002/prot.24016 (2012).CAS
Article
PubMed
Google Scholar
15.Marziale, F. et al. Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature. FEBS J 275, 5367–5382. https://doi.org/10.1111/j.1742-4658.2008.06666.x (2008).CAS
Article
PubMed
Google Scholar
16.Pucciarelli, S., Miceli, C. & Melki, R. Heterologous expression and folding analysis of a beta-tubulin isotype from the Antarctic ciliate Euplotes focardii. Eur J Biochem 269, 6271–6277 (2002).CAS
Article
Google Scholar
17.Gromer, S., Urig, S. & Becker, K. The thioredoxin system–from science to clinic. Med Res Rev 24, 40–89. https://doi.org/10.1002/med.10051 (2004).CAS
Article
PubMed
Google Scholar
18.Birben, E., Sahiner, U. M., Sackesen, C., Erzurum, S. & Kalayci, O. Oxidative stress and antioxidant defense. World Allergy Organ J 5, 9–19. https://doi.org/10.1097/WOX.0b013e3182439613 (2012).CAS
Article
PubMed
PubMed Central
Google Scholar
19.Alin, P., Danielson, U. H. & Mannervik, B. 4-Hydroxyalk-2-enals are substrates for glutathione transferase. FEBS Lett 179, 267–270 (1985).CAS
Article
Google Scholar
20.Juganson, K. et al. Mechanisms of toxic action of silver nanoparticles in the protozoan Tetrahymena thermophila: From gene expression to phenotypic events. Environ Pollut 225, 481–489. https://doi.org/10.1016/j.envpol.2017.03.013 (2017).CAS
Article
PubMed
Google Scholar
21.Clark, M. S., Fraser, K. P. & Peck, L. S. Antarctic marine molluscs do have an HSP70 heat shock response. Cell Stress Chaperones 13, 39–49. https://doi.org/10.1007/s12192-008-0014-8 (2008).CAS
Article
PubMed
PubMed Central
Google Scholar
22.Tomanek, L. The heat-shock response: its variation, regulation and ecological importance in intertidal gastropods (genus Tegula). Integr Comp Biol 42, 797–807. https://doi.org/10.1093/icb/42.4.797 (2002).CAS
Article
PubMed
Google Scholar
23.Morimoto, R. I., Kline, M. P., Bimston, D. N. & Cotto, J. J. The heat-shock response: regulation and function of heat-shock proteins and molecular chaperones. Essays Biochem 32, 17–29 (1997).CAS
PubMed
Google Scholar
24.Gonzalez-Aravena, M. et al. HSP70 from the Antarctic sea urchin Sterechinus neumayeri: molecular characterization and expression in response to heat stress. Biol Res 51, 8. https://doi.org/10.1186/s40659-018-0156-9 (2018).CAS
Article
PubMed
PubMed Central
Google Scholar
25.Hofmann, G. E., Buckley, B. A., Airaksinen, S., Keen, J. E. & Somero, G. N. Heat-shock protein expression is absent in the antarctic fish Trematomus bernacchii (family Nototheniidae). J Exp Biol 203, 2331–2339 (2000).CAS
Article
Google Scholar
26.La Terza, A., Papa, G., Miceli, C. & Luporini, P. Divergence between two Antarctic species of the ciliate Euplotes, E. focardii and E. nobilii, in the expression of heat-shock protein 70 genes. Mol Ecol 10, 1061–1067. https://doi.org/10.1046/j.1365-294x.2001.01242.x (2001).27.Klobutcher, L. A. & Farabaugh, P. J. Shifty ciliates: frequent programmed translational frameshifting in euplotids. Cell 111, 763–766 (2002).CAS
Article
Google Scholar
28.Lobanov, A. V. et al. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat Struct Mol Biol 24, 61–68. https://doi.org/10.1038/nsmb.3330 (2017).CAS
Article
PubMed
Google Scholar
29.Coordinators, N. R. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 45, D12–D17. https://doi.org/10.1093/nar/gkw1071 (2017).CAS
Article
Google Scholar
30.Pucciarelli, S. et al. Microbial consortium associated with the antarctic marine ciliate Euplotes focardii: an investigation from genomic sequences. Microb Ecol 70, 484–497. https://doi.org/10.1007/s00248-015-0568-9 (2015).CAS
Article
PubMed
PubMed Central
Google Scholar
31.Klobutcher, L. A. et al. Conserved DNA sequences adjacent to chromosome fragmentation and telomere addition sites in Euplotes crassus. Nucleic Acids Res 26, 4230–4240. https://doi.org/10.1093/nar/26.18.4230 (1998).CAS
Article
PubMed
PubMed Central
Google Scholar
32.Aeschlimann, S. H. et al. The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. Genome Biol Evol 6, 1707–1723. https://doi.org/10.1093/gbe/evu139 (2014).CAS
Article
PubMed
PubMed Central
Google Scholar
33.Swart, E. C. (personal communication).34.Cavalcanti, A. R., Stover, N. A., Orecchia, L., Doak, T. G. & Landweber, L. F. Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma 113, 69–76. https://doi.org/10.1007/s00412-004-0295-3 (2004).CAS
Article
PubMed
Google Scholar
35.Lozupone, C. A., Knight, R. D. & Landweber, L. F. The molecular basis of nuclear genetic code change in ciliates. Curr Biol 11, 65–74. https://doi.org/10.1016/s0960-9822(01)00028-8 (2001).CAS
Article
PubMed
Google Scholar
36.Salas-Marco, J. et al. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol 26, 438–447. https://doi.org/10.1128/MCB.26.2.438-447.2006 (2006).CAS
Article
PubMed
PubMed Central
Google Scholar
37.Klobutcher, L. A. Sequencing of random Euplotes crassus macronuclear genes supports a high frequency of +1 translational frameshifting. Eukaryot Cell 4, 2098–2105. https://doi.org/10.1128/EC.4.12.2098-2105.2005 (2005).CAS
Article
PubMed
PubMed Central
Google Scholar
38.Wang, R., Xiong, J., Wang, W., Miao, W. & Liang, A. High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. Sci Rep 6, 21139. https://doi.org/10.1038/srep21139 (2016).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
39.Turanov, A. A. et al. Genetic code supports targeted insertion of two amino acids by one codon. Science 323, 259–261. https://doi.org/10.1126/science.1164748 (2009).CAS
Article
PubMed
PubMed Central
Google Scholar
40.Maehigashi, T., Dunkle, J. A., Miles, S. J. & Dunham, C. M. Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops. Proc Natl Acad Sci U S A 111, 12740–12745. https://doi.org/10.1073/pnas.1409436111 (2014).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
41.Miceli, C., Ballarini, P., Di Giuseppe, G., Valbonesi, A. & Luporini, P. Identification of the tubulin gene family and sequence determination of one beta-tubulin gene in a cold-poikilotherm protozoan, the antarctic ciliate Euplotes focardii. J Eukaryot Microbiol 41, 420–427. https://doi.org/10.1111/j.1550-7408.1994.tb06100.x (1994).CAS
Article
PubMed
Google Scholar
42.Ricci, F. et al. The sub-chromosomic macronuclear pheromone genes of the ciliate Euplotes raikovi: comparative structural analysis and insights into the mechanism of expression. J Eukaryot Microbiol 66, 376–384. https://doi.org/10.1111/jeu.12677 (2019).CAS
Article
PubMed
Google Scholar
43.Wang, R., Liu, J., Di Giuseppe, G. & Liang, A. UAA and UAG may Encode Amino Acid in Cathepsin B Gene of Euplotes octocarinatus. J Eukaryot Microbiol 67, 144–149. https://doi.org/10.1111/jeu.12755 (2020).CAS
Article
PubMed
Google Scholar
44.Heaphy, S. M., Mariotti, M., Gladyshev, V. N., Atkins, J. F. & Baranov, P. V. Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in condylostoma magnum. Mol Biol Evol 33, 2885–2889. https://doi.org/10.1093/molbev/msw166 (2016).CAS
Article
PubMed
PubMed Central
Google Scholar
45.Swart, E. C., Serra, V., Petroni, G. & Nowacki, M. Genetic codes with no dedicated stop codon: context-dependent translation termination. Cell 166, 691–702. https://doi.org/10.1016/j.cell.2016.06.020 (2016).CAS
Article
PubMed
PubMed Central
Google Scholar
46.Roy, B., Leszyk, J. D., Mangus, D. A. & Jacobson, A. Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3. Proc Natl Acad Sci U S A 112, 3038–3043. https://doi.org/10.1073/pnas.1424127112 (2015).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
47.Dunn, J. G., Foo, C. K., Belletier, N. G., Gavis, E. R. & Weissman, J. S. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife 2, e01179. https://doi.org/10.7554/eLife.01179 (2013).Article
PubMed
PubMed Central
Google Scholar
48.Frechin, M., Duchene, A. M. & Becker, H. D. Translating organellar glutamine codons: a case by case scenario?. RNA Biol 6, 31–34. https://doi.org/10.4161/rna.6.1.7564 (2009).CAS
Article
PubMed
Google Scholar
49.Wilcox, M. & Nirenberg, M. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc Natl Acad Sci U S A 61, 229–236. https://doi.org/10.1073/pnas.61.1.229 (1968).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
50.Detrich, H. W. 3rd., Fitzgerald, T. J., Dinsmore, J. H. & Marchese-Ragona, S. P. Brain and egg tubulins from antarctic fishes are functionally and structurally distinct. J Biol Chem 267, 18766–18775 (1992).CAS
Article
Google Scholar
51.Detrich, H. W. 3rd., Johnson, K. A. & Marchese-Ragona, S. P. Polymerization of Antarctic fish tubulins at low temperatures: energetic aspects. Biochemistry 28, 10085–10093 (1989).CAS
Article
Google Scholar
52.Wloga, D. et al. Glutamylation on alpha-tubulin is not essential but affects the assembly and functions of a subset of microtubules in Tetrahymena thermophila. Eukaryot Cell 7, 1362–1372. https://doi.org/10.1128/EC.00084-08 (2008).CAS
Article
PubMed
PubMed Central
Google Scholar
53.Eisen, J. A. et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 4, e286. https://doi.org/10.1371/journal.pbio.0040286 (2006).CAS
Article
PubMed
PubMed Central
Google Scholar
54.Aury, J. M. et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444, 171–178. https://doi.org/10.1038/nature05230 (2006).ADS
CAS
Article
PubMed
Google Scholar
55.Pucciarelli, S. et al. Distinct functional roles of beta-tubulin isotypes in microtubule arrays of Tetrahymena thermophila, a model single-celled organism. PLoS ONE 7, e39694. https://doi.org/10.1371/journal.pone.0039694 (2012).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
56.Pucciarelli, S. et al. Tubulin folding: the special case of a beta-tubulin isotype from the Antarctic psychrophilic ciliate Euplotes focardii. Polar Biol 36, 1833–1838. https://doi.org/10.1007/s00300-013-1390-9 (2013).Article
Google Scholar
57.Pucci, F. & Rooman, M. Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 42, 117–128. https://doi.org/10.1016/j.sbi.2016.12.007 (2017).CAS
Article
PubMed
Google Scholar
58.Aqvist, J., Isaksen, G. V. & Brandsdal, B. O. Computation of enzyme cold adaptation. Nat Rev Chem 1, 0051. https://doi.org/10.1038/s41570-017-0051 (2017).CAS
Article
Google Scholar
59.Lesser, M. P. Oxidative stress in marine environments: biochemistry and physiological ecology. Annu Rev Physiol 68, 253–278. https://doi.org/10.1146/annurev.physiol.68.040104.110001 (2006).CAS
Article
PubMed
Google Scholar
60.McCord, J. M. & Fridovich, I. Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein). J Biol Chem 244, 6049–6055 (1969).61.McCord, J. M. & Fridovich, I. Superoxide dismutase: the first twenty years (1968–1988). Free Radic Biol Med 5, 363–369 (1988).CAS
Article
Google Scholar
62.Miller, A. F. Superoxide dismutases: ancient enzymes and new insights. FEBS Lett 586, 585–595. https://doi.org/10.1016/j.febslet.2011.10.048 (2012).CAS
Article
PubMed
Google Scholar
63.Benov, L. T. & Fridovich, I. Escherichia coli expresses a copper- and zinc-containing superoxide dismutase. J Biol Chem 269, 25310–25314 (1994).CAS
Article
Google Scholar
64.Steinman, H. M. & Ely, B. Copper-zinc superoxide dismutase of Caulobacter crescentus: cloning, sequencing, and mapping of the gene and periplasmic location of the enzyme. J Bacteriol 172, 2901–2910. https://doi.org/10.1128/jb.172.6.2901-2910.1990 (1990).CAS
Article
PubMed
PubMed Central
Google Scholar
65.Antonyuk, S. V., Strange, R. W., Marklund, S. L. & Hasnain, S. S. The structure of human extracellular copper-zinc superoxide dismutase at 1.7 A resolution: insights into heparin and collagen binding. J Mol Biol 388, 310–326. https://doi.org/10.1016/j.jmb.2009.03.026 (2009).66.Marklund, S. L. Extracellular superoxide dismutase and other superoxide dismutase isoenzymes in tissues from nine mammalian species. Biochem J 222, 649–655. https://doi.org/10.1042/bj2220649 (1984).CAS
Article
PubMed
PubMed Central
Google Scholar
67.Bannister, J. V., Bannister, W. H. & Rotilio, G. Aspects of the structure, function, and applications of superoxide dismutase. CRC Crit Rev Biochem 22, 111–180 (1987).CAS
Article
Google Scholar
68.James, E. R. Superoxide dismutase. Parasitol Today 10, 481–484. https://doi.org/10.1016/0169-4758(94)90161-9 (1994).CAS
Article
PubMed
Google Scholar
69.Ferro, D. et al. Cu, Zn superoxide dismutases from Tetrahymena thermophila: molecular evolution and gene expression of the first line of antioxidant defenses. Protist 166, 131–145. https://doi.org/10.1016/j.protis.2014.12.003 (2015).CAS
Article
PubMed
Google Scholar
70.Arnaiz, O. & Sperling, L. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res 39, D632-636. https://doi.org/10.1093/nar/gkq918 (2011).CAS
Article
PubMed
Google Scholar
71.Fink, R. C. & Scandalios, J. G. Molecular evolution and structure–function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases. Arch Biochem Biophys 399, 19–36. https://doi.org/10.1006/abbi.2001.2739 (2002).CAS
Article
PubMed
Google Scholar
72.Lee, Y. M., Friedman, D. J. & Ayala, F. J. Superoxide dismutase: an evolutionary puzzle. Proc Natl Acad Sci U S A 82, 824–828. https://doi.org/10.1073/pnas.82.3.824 (1985).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
73.Pischedda, A. et al. Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. Sci Rep 8, 14721. https://doi.org/10.1038/s41598-018-33127-1 (2018).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
74.Yang, G. et al. Characterization of the first eukaryotic cold-adapted patatin-like phospholipase from the psychrophilic Euplotes focardii: Identification of putative determinants of thermal-adaptation by comparison with the homologous protein from the mesophilic Euplotes crassus. Biochimie 95, 1795–1806. https://doi.org/10.1016/j.biochi.2013.06.008 (2013).CAS
Article
PubMed
Google Scholar
75.Li, J., Zhou, L., Lin, X., Yi, Z. & Al-Rasheid, K. A. Characterizing dose-responses of catalase to nitrofurazone exposure in model ciliated protozoan Euplotes vannus for ecotoxicity assessment: enzyme activity and mRNA expression. Ecotoxicol Environ Saf 100, 294–302. https://doi.org/10.1016/j.ecoenv.2013.08.021 (2014).CAS
Article
PubMed
Google Scholar
76.Prast-Nielsen, S., Huang, H. H. & Williams, D. L. Thioredoxin glutathione reductase: its role in redox biology and potential as a target for drugs against neglected diseases. Biochim Biophys Acta 1262–1271, 2011. https://doi.org/10.1016/j.bbagen.2011.06.024 (1810).CAS
Article
Google Scholar
77.Kabani, M. & Martineau, C. N. Multiple hsp70 isoforms in the eukaryotic cytosol: mere redundancy or functional specificity?. Curr Genomics 9, 338–248. https://doi.org/10.2174/138920208785133280 (2008).CAS
Article
PubMed
PubMed Central
Google Scholar
78.La Terza, A., Miceli, C. & Luporini, P. The gene for the heat-shock protein 70 of Euplotes focardii, an Antarctic psychrophilic ciliate. Antarct. Sci. 16, 23–28. https://doi.org/10.1017/S0954102004001774 (2004).ADS
Article
Google Scholar
79.Chen, X. et al. Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. Mol Ecol Resour 19, 1292–1308. https://doi.org/10.1111/1755-0998.13023 (2019).CAS
Article
PubMed
PubMed Central
Google Scholar
80.Chen, Z. et al. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc Natl Acad Sci U S A 105, 12944–12949. https://doi.org/10.1073/pnas.0802432105 (2008).ADS
Article
PubMed
PubMed Central
Google Scholar
81.Li, Y. et al. Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis. BMC Genomics 20, 624. https://doi.org/10.1186/s12864-019-5988-3 (2019).CAS
Article
PubMed
PubMed Central
Google Scholar
82.Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).CAS
Article
PubMed
PubMed Central
Google Scholar
83.Andrews, S. (2010).84.Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19, 455–477. https://doi.org/10.1089/cmb.2012.0021 (2012).MathSciNet
CAS
Article
PubMed
PubMed Central
Google Scholar
85.Nikolenko, S. I., Korobeynikov, A. I. & Alekseyev, M. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 14 Suppl 1, S7. https://doi.org/10.1186/1471-2164-14-S1-S7 (2013).86.Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075. https://doi.org/10.1093/bioinformatics/btt086 (2013).CAS
Article
PubMed
PubMed Central
Google Scholar
87.Boscaro, V., Husnik, F., Vannini, C. & Keeling, P. J. Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses. Proc Biol Sci 286, 20190693. https://doi.org/10.1098/rspb.2019.0693 (2019).Article
PubMed
PubMed Central
Google Scholar
88.Serra, V. et al. Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov. Sci Rep 10, 20311. https://doi.org/10.1038/s41598-020-76348-z (2020).89.Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34, W435-439. https://doi.org/10.1093/nar/gkl200 (2006).CAS
Article
PubMed
PubMed Central
Google Scholar
90.Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323. https://doi.org/10.1186/1471-2105-12-323 (2011).CAS
Article
PubMed
PubMed Central
Google Scholar
91.Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676. https://doi.org/10.1093/bioinformatics/bti610 (2005).CAS
Article
PubMed
Google Scholar
92.Gotz, S. et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36, 3420–3435. https://doi.org/10.1093/nar/gkn176 (2008).CAS
Article
PubMed
PubMed Central
Google Scholar
93.Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061–1067. https://doi.org/10.1093/bioinformatics/btm071 (2007).CAS
Article
PubMed
Google Scholar
94.Laslett, D. & Canback, B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32, 11–16. https://doi.org/10.1093/nar/gkh152 (2004).CAS
Article
PubMed
PubMed Central
Google Scholar
95.Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res 36, W70-74. https://doi.org/10.1093/nar/gkn188 (2008).CAS
Article
PubMed
PubMed Central
Google Scholar
96.Popenda, M. et al. Automated 3D structure composition for large RNAs. Nucleic Acids Res 40, e112. https://doi.org/10.1093/nar/gks339 (2012).CAS
Article
PubMed
PubMed Central
Google Scholar
97.Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152. https://doi.org/10.1093/bioinformatics/bts565 (2012).CAS
Article
PubMed
PubMed Central
Google Scholar
98.Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659. https://doi.org/10.1093/bioinformatics/btl158 (2006).CAS
Article
PubMed
Google Scholar
99.Shigematsu, M. et al. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res 45, e70. https://doi.org/10.1093/nar/gkx005 (2017).CAS
Article
PubMed
PubMed Central
Google Scholar
100.Bushnell, B., Rood, J. & Singer, E. BBMerge: accurate paired shotgun read merging via overlap. PLoS ONE 12, e0185056. https://doi.org/10.1371/journal.pone.0185056 (2017).CAS
Article
PubMed
PubMed Central
Google Scholar
101.Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011 17, 3. https://doi.org/10.14806/ej.17.1.200 (2011).102.Holmes, A. D., Howard, J. M., Chan, P. P. & Lowe, T. M. tRNA Analysis of eXpression (tRAX): A tool for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications. (Submitted) (2020).103.Sievers, F. & Higgins, D. G. Clustal omega. Curr Protoc Bioinformatics 48, 3 13 11–16. https://doi.org/10.1002/0471250953.bi0313s48 (2014).104.Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).CAS
Article
PubMed
PubMed Central
Google Scholar
105.Webb, B. & Sali, A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinform. 54, 5 6 1–5 6 37. https://doi.org/10.1002/cpbi.3 (2016).106.Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46, W296–W303. https://doi.org/10.1093/nar/gky427 (2018).CAS
Article
PubMed
PubMed Central
Google Scholar
107.Ichikawa, M. et al. Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins. Proc Natl Acad Sci U S A 116, 19930–19938. https://doi.org/10.1073/pnas.1911119116 (2019).CAS
Article
PubMed
PubMed Central
Google Scholar
108.Chaaban, S. et al. The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Dev Cell 47, 191–204 e198. https://doi.org/10.1016/j.devcel.2018.08.023 (2018).109.Kikkawa, M. et al. Switch-based mechanism of kinesin motors. Nature 411, 439–445. https://doi.org/10.1038/35078000 (2001).ADS
CAS
Article
PubMed
Google Scholar
110.Howes, S. C. et al. Structural differences between yeast and mammalian microtubules revealed by cryo-EM. J Cell Biol 216, 2669–2677. https://doi.org/10.1083/jcb.201612195 (2017).CAS
Article
PubMed
PubMed Central
Google Scholar
111.Ma, M. et al. Structure of the Decorated Ciliary Doublet Microtubule. Cell 179, 909–922 e912. https://doi.org/10.1016/j.cell.2019.09.030 (2019).112.Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001 (2015).ADS
Article
Google Scholar
113.Morrison, T. B., Weis, J. J. & Wittwer, C. T. Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24, 954–958, 960, 962 (1998).114.Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29, e45. https://doi.org/10.1093/nar/29.9.e45 (2001).CAS
Article
PubMed
PubMed Central
Google Scholar
115.Pfaffl, M. W., Horgan, G. W. & Dempfle, L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30, e36. https://doi.org/10.1093/nar/30.9.e36 (2002).Article
PubMed
PubMed Central
Google Scholar More