Hand, S.C. Metabolic dormancy in aquatic invertebrates. In Advances in Comparative and Environmental Physiology, Vol. 8 (ed. Gilles, R.) 1–50. https://doi.org/10.1007/978-3-642-75900-0_1 (1991).
Cáceres, C. E. Dormancy in Invertebrates. Invertebr. Biol. 116(4), 371–383. https://doi.org/10.2307/3226870 (1997).
Google Scholar
Wilsterman, K., Ballinger, M. A. & Williams, C. M. A unifying, eco-physiological framework for animal dormancy. Funct. Ecol. 35, 11–31. https://doi.org/10.1111/1365-2435.13718 (2021).
Google Scholar
Bertolani, R., Guidetti, R., Altiero, T., Nelson, D. R. & Rebecchi, L. Dormancy in Freshwater Tardigrades. In Dormancy in Aquatic Organisms. Theory, Human Use and Modeling. Monographiae Biologicae Vol. 92 (eds Alekseev, V. & Pinel-Alloul, B.) (Springer, Cham, 2019). https://doi.org/10.1007/978-3-030-21213-1_3.
Google Scholar
Guidetti, R., Altiero, T. & Rebecchi, L. On dormancy strategies in tardigrades. J. Insect Physiol. 57(5), 567–576. https://doi.org/10.1016/j.jinsphys.2011.03.003 (2011).
Google Scholar
Hahn, D. A. & Denlinger, D. L. Energetics of insect diapause. Annu. Rev. Entomol. 56, 103–121. https://doi.org/10.1146/annurev-ento-112408-085436 (2011).
Google Scholar
Ragland, G. J. & Keep, E. Comparative transcriptomics support evolutionary convergence of diapause responses across Insecta. Physiol. Entomol. 42(3), 246–256. https://doi.org/10.1111/phen.12193 (2017).
Google Scholar
Wang, Y., Ezemaduka, A. N., Tang, Y. & Chang, Z. Understanding the mechanism of the dormant dauer formation of C. elegans: From genetics to biochemistry. IUBMB Life 61(6), 607–12. https://doi.org/10.1002/iub.211 (2009).
Google Scholar
Dias, I. B., Bouma, H. R. & Henning, R. H. Unraveling the big sleep: Molecular aspects of stem cell dormancy and hibernation. Front. Physiol. 12, 624950. https://doi.org/10.3389/fphys.2021.624950 (2021).
Google Scholar
Storey, K. B. & Storey, J. M. Metabolic regulation and gene expression during aestivation. Prog. Mol. Subcell. Biol. 49, 25–45. https://doi.org/10.1007/978-3-642-02421-4_2 (2010).
Google Scholar
Hand, S. C., Denlinger, D. L., Podrabsky, J. E. & Roy, R. Mechanisms of animal diapause: Recent developments from nematodes, crustaceans, insects, and fish. Am. J. Physiol. Regul. Integr. Comp. Physiol. 310(11), R1193–R1211. https://doi.org/10.1152/ajpregu.00250.2015 (2016).
Google Scholar
Ikeda, H., Ohtsu, K. & Uye, S. I. Fine structure, histochemistry, and morphogenesis during excystment of the podocysts of the giant jellyfish Nemopilema nomurai (Scyphozoa, Rhizostomeae). Biol. Bull. 221(3), 248–260 (2011).
Google Scholar
Bushnell, J. H. & Rao, K. S. Dormant or quiescent stages and structures among the Ectoprocta: Physical and chemical factors affecting viability and germination of statoblasts. Trans. Am. Microsc. Soc. 93, 524–543. https://doi.org/10.2307/3225156 (1974).
Google Scholar
Hyman, L. H. The Invertebrates: Acanthocephala, Aschelminthes and Entoprocta Vol. III (McGraw-Hill, 1951).
Mukai, H. & Toshiki, M. Studies on the regeneration of an entoproct, Barentsia discreta. J. Exp. Zool. 205(2), 261–276. https://doi.org/10.1002/jez.1402050210 (1978).
Google Scholar
Nakauchi, M. Asexual development of ascidians: Its biological significance, diversity, and morphogenesis. Am. Zool. 22(4), 753–763. https://doi.org/10.1093/icb/22.4.753 (1982).
Google Scholar
Hyams, Y., Paz, G., Rabinowitz, C. & Rinkevich, B. Insights into the unique torpor of Botrylloides leachi, a colonial urochordate. Dev. Biol. 428(1), 101–117. https://doi.org/10.1016/j.ydbio.2017.05.020 (2017).
Google Scholar
Brown, C. J. D. A limnological study of certain fresh-water Polyzoa with special reference to their statoblasts. Trans. Am. Microsc. Soc. 52, 271–313 (1933).
Google Scholar
Mukai, H. Development of freshwater bryozoans (Phylactolaemata). In Developmental Biology of Freshwater Invertebrates (eds Harrison, R. W. & Cowden, R. R.) 535–576 (Alan R. Liss Inc., 1982).
Wood, T. S. Phyla ectoprocta and entoprocta (Bryozoans). In Freshwater Invertebrates (eds Thorp, J. H. & Covich, A. P.) 327–345 (Academic Press, 2015). https://doi.org/10.1016/B978-0-12-385026-3.00016-4.
Google Scholar
Simpson, T. L. The Cell Biology of Sponges (Springer, New York, 1984). https://doi.org/10.1007/978-1-4612-5214-6.
Google Scholar
Alié, A., Hiebert, L. S., Scelzo, M. & Tiozzo, S. The eventful history of nonembryonic development in tunicates. J. Exp. Zool. Part B Mol. Dev. Evol. 33(3), 181–217. https://doi.org/10.1002/jez.b.22940 (2020).
Google Scholar
Brown, F. D. & Swalla, B. J. Evolution and development of budding by stem cells: Ascidian coloniality as a case study. Dev. Biol. 3692, 151–162 (2012).
Google Scholar
Kawamura, K. & Fujiwara, S. Cellular and molecular characterization of transdifferentiation in the process of morphallaxis of budding tunicates. Semin. Cell Biol. 6, 117–126 (1995).
Google Scholar
Kassmer, S. H., Langenbacher, A. D. & De Tomaso, A. W. Integrin-alpha-6+ candidate stem cells are responsible for whole body regeneration in the invertebrate chordate Botrylloides diegensis. Nat. Commun. 11(1), 4435–4511. https://doi.org/10.1038/s41467-020-18288-w (2020).
Google Scholar
Freeman, G. The role of blood cells in the process of asexual reproduction in the tunicate Perophora viridis. J. Exp. Zool. 156, 157–183 (1964).
Google Scholar
Kürn, U., Rendulic, S., Tiozzo, S. & Lauzon, R. J. Asexual propagation and regeneration in colonial ascidians. Biol. Bull. 221(1), 43–61. https://doi.org/10.1086/BBLv221n1p43 (2011).
Google Scholar
Sköld, H. N., Obst, M., Sköld, M. & Åkesson, B. Stem cells in asexual reproduction of marine invertebrates. In Stem Cells in Marine Organisms (eds Rinkevich, B. & Matranga, V.) 105–137 (Springer, Dordrecht, 2009).
Google Scholar
Tiozzo, S., Brown, F. D. & De Tomaso, A. W. Regeneration and stem cells in ascidians. In Stem Cells (ed. Bosch, T. C. G.) (Springer, Dordrecht, 2008). https://doi.org/10.1007/978-1-4020-8274-0_6.
Google Scholar
Mukai, H., Koyama, H. & Watanabe, H. Studies on the reproduction of three species of Perophora (Ascidiacea). Biol. Bull. 164(2), 251–266 (1983).
Google Scholar
Huxley, J. Memoirs: studies in dedifferentiation: II. Dedifferentiation and resorption in Perophora. Q. J. Microsc. Sci. s2-65(260), 643–697 (1921).
Huxley, J. Studies in dedifferentiation. VI. Reduction phenomena in Clavelina lepadiformis. Pubb. Staz. Zool. Napoli. 7, 1–34 (1926).
Turon, X. Periods of nonfeeding in Polysyncraton-lacazei (Ascidiacea, Didemnidae)—A process. Mar. Biol. 112, 647–655 (1992).
Google Scholar
Delsuc, F. et al. A phylogenomic framework and timescale for comparative studies of tunicates. BMC Biol. 16, 39 (2018).
Google Scholar
Giard, M. A. & Caullery, M. On the hibernation of Clavelina lepadiformis, Müller. Ann. Mag. Nat. Hist. 18(108), 485–486. https://doi.org/10.1080/00222939608680499 (1896).
Google Scholar
Orton, J. H. The production of living Clavellina Zooids in winter by experiment. Nature 107, 75. https://doi.org/10.1038/107075a0 (1921).
Google Scholar
Della, Valle P. Studii sui rapporti fra differenziazione e rigenerazione. 4. Bollettino Della Società Dei Naturalisti in Napoli 7, 1–37 (1915).
Scelzo, M. et al. Novel budding mode in Polyandrocarpa zorritensis: a model for comparative studies on asexual development and whole body regeneration. EvoDevo https://doi.org/10.1186/s13227-019-0121-x (2019).
Google Scholar
Berrill, N. J. Regeneration and budding in tunicates. Biol. Rev. 26, 456–475. https://doi.org/10.1111/j.1469-185X.1951.tb01207.x/full (1951).
Google Scholar
Kilpatrick, K. A., Podestá, G. P. & Evans, R. Overview of the NOAA/NASA advanced very high resolution radiometer Pathfinder algorithm for sea surface temperature and associated matchup database. J. Geophys. Res. 106(C5), 9179–9197. https://doi.org/10.1029/1999JC000065 (2001).
Google Scholar
Berrill, N. J. & Cohen, A. Regeneration in Clavelina lepadiformis. J. Exp. Biol. 13(3), 352–362. https://doi.org/10.1242/jeb.13.3.352 (1936).
Google Scholar
Jiménez-Merino, J. et al. Putative stem cells in the hemolymph and in the intestinal submucosa of the solitary ascidian Styela plicata. EvoDevo https://doi.org/10.1186/s13227-019-0144-3 (2019).
Google Scholar
Du, Q., Luu, P.-L., Stirzaker, C. & Clark, S. J. Methyl-CpG-binding domain proteins: Readers of the epigenome. Epigenomics UK 7, 1051–1073 (2015).
Google Scholar
Rea, S. & Akhtar, A. MSL proteins and the regulation of gene expression. In DNA Methylation: Development, Genetic Disease and Cancer: Current Topics in Microbiology and Immunology Vol. 310 (eds Doerfler, W. & Böhm, P.) (Springer, 2006). https://doi.org/10.1007/3-540-31181-5_7.
Google Scholar
Orton, J. H. Preliminary account of a contribution to an evaluation of the sea. J. Mar. Biol. Assoc. UK 10(2), 312–326. https://doi.org/10.1017/S0025315400007815 (1914).
Google Scholar
Mukai, H. Histological and histochemical studies of two compound ascidians, Clavelina lepadiformis and Diazona violacea, with special reference to the trophocytes, ovary and pyloric gland. Sci. Rep. Fac. Educ. Gunma Univ. 26, 37–77 (1977).
de Caralt, S., López-Legentil, S., Tarjuelo, I., Uriz, M. J. & Turon, X. Contrasting biological traits of Clavelina lepadiformis (Ascidiacea) populations from inside and outside harbours in the western Mediterranean. Mar. Ecol. Prog. Ser. 244, 125–137 (2002).
Google Scholar
Turon, X. A new mode of colony multiplication by modified budding in the ascidian Clavelina gemmae n. sp. (Clavelinidae). Invertebr. Biol. 124(3), 273–283. https://doi.org/10.1111/j.1744-7410.2005.00025.x (2005).
Google Scholar
Pyo, J. & Shin, S. A new record of invasive alien colonial tunicate Clavelina lepadiformis (Ascidiacea: Aplousobranchia: Clavelinidae) in Korea. Anim. Syst. Evol. Divers. 27, 197–200 (2011).
Google Scholar
Reinhardt, J. et al. First record of the non-native light bulb tunicate Clavelina lepadiformis (Müller, 1776) in the northwest Atlantic. Aquat. Invasions 5(2), 185–190. https://doi.org/10.3391/ai.2010.5.2.09 (2010).
Google Scholar
Turon, X., Tarjuelo, I., Duran, S. & Pascual, M. Characterising invasion processes with genetic data: An Atlantic clade of Clavelina lepadiformis (Ascidiacea) introduced into Mediterranean harbours. Hydrobiologia 503(1–3), 29–35. https://doi.org/10.1023/b:hydr.0000008481.10705.c2 (2003).
Google Scholar
Van Name, W. G. The North and South American ascidians. Bull. Am. Mus. Nat. Hist. 84, 1–476 (1945).
Carman, M. et al. Ascidians at the Pacific and Atlantic entrances to the Panama Canal. Aquat. Invasions 6(4), 371–380. https://doi.org/10.3391/ai.2011.6.4.02 (2011).
Google Scholar
Holman, L. E. et al. Managing human-mediated range shifts: Understanding spatial, temporal and genetic variation in marine non-native species. Philos. Trans. R. Soc. B 377, 20210025 (2022).
Google Scholar
Lambert, C. C. & Lambert, G. Persistence and differential distribution of nonindigenous ascidians in harbors of the Southern California Bight. Marine Ecology Progress Series 259, 145–161. https://doi.org/10.3354/meps259145 (2003).
Google Scholar
Brunetti, R. Polyandrocarpa zorritensis (Van Name, 1931). A colonial ascidian new to the Mediterranean record. Vie et Milieu 28–29, 647–652 (1978).
Brunetti, R. & Mastrototaro, F. The non-indigenous stolidobranch ascidian Polyandrocarpa zorritensis in the Mediterranean: Description, larval morphology and pattern of vascular budding. Zootaxa 528, 1–8 (2004).
Google Scholar
Mastrototaro, F., D’Onghia, G. & Tursi, A. Spatial and seasonal distribution of ascidians in a semi-enclosed basin of the Mediterranean Sea. J. Mar. Biol. Assoc. UK 88, 1053–1061 (2008).
Google Scholar
Stabili, L., Licciano, M., Longo, C., Lezzi, M. & Giangrande, A. The Mediterranean non- indigenous ascidian Polyandrocarpa zorritensis: Microbiological accumulation capability and environmental implications. Mar. Pollut. Bull. 101, 146–152 (2015).
Google Scholar
Turon, X. & Becerro, M. A. Growth and survival of several ascidian species from the northwestern Mediterranean. Mar. Ecol. Prog. Ser. 82, 235–247 (1992).
Google Scholar
Sumida, P. Y. G. et al. Pressure tolerance of tadpole larvae of the Atlantic ascidian Polyandrocarpa zorritensis: Potential for deep-sea invasion. Braz. J. Oceanogr. 63, 515–520 (2015).
Google Scholar
Vázquez, E. & Young, C. M. Responses of compound ascidian larvae to haloclines. Mar. Ecol. Prog. Ser. 133, 179–190 (1996).
Google Scholar
Vázquez, E. & Young, C. M. Ontogenetic changes in phototaxis during larval life of the Ascidian Polyandrocarpa zorritensis (Van Name, 1931). J. Exp. Mar. Biol. Ecol. 231, 267–277 (1998).
Google Scholar
Brien, P. & Brien-Gavage, E. Contribution à l’étude de la Blastogénèse des Tuniciers: III: Bourgeonnement de Clavelina Lepadiformis Müller. Recueil de L’Institut Zoologique Torley-Rousseau 1–56 (1927).
Fujimoto, H. & Watanabe, H. The characterization of granular amoebocytes and their possible roles in the asexual reproduction of the polystyelid ascidian, Polyzoa vesiculiphora. J. Morphol. 150(3), 623–637. https://doi.org/10.1002/jmor.1051500303 (1976).
Google Scholar
Cima, F., Franchi, N. & Ballarin, L. Origin and functions of tunicate hemocytes. In The Evolution of the Immune System (ed. Malagoli, D.) 29–49 (Elsevier, 2016). https://doi.org/10.1016/B978-0-12-801975-7/00002-5.
Google Scholar
Kerb, H. Biologische Beiträge zur Frage der Überwinterung der Ascidien. Arch. Mikrosk. Anat. 72(1), 386–414 (1908).
Google Scholar
Driesch, H. Studien über das Regulationsvermögen de Organismen. 6. Die Restitutionen der Clavellina lepadiformis. Arch. F. Entw.-Mech. 14, 247–287 (1902).
Google Scholar
Schultz, E. Über Reductionen. III. Die Reduction und Regeneration des abgeschnitten Kiemenkorbes von Clavellina lepadiformis. Arch. Entw. Mech. Org. 24, 503–523 (1907).
Spek, J. Über die Winterknospenentwicklung, Regeneration und Reduktion bei Clavellina lepadiformis und die Bedeutung besonderer “omnipotenter” Zellelemente für diese Vorgänge. Wilhelm Roux’Archiv Entwicklungsmechanik der Org 111(119), 172 (1927).
Brien, P. Contribution à l’étude de la régéneration naturelle et expérimentale chez les Clavelinidae. Soc. R. Zool. Belg. Ann LXI, 19–112 (1930).
Ries, E. Die Tropfenzellen und ihre Bedeutung für die Tunicabildung bei Clavelina. Wilhelm Roux Arch. Entwickl. Mech. Org. 137(3), 363–371. https://doi.org/10.1007/BF00593066 (1937).
Google Scholar
Fischer, I. Über das Verhalten des stolonialen Gewebes der Ascidie Clavelina lepadiformis in vitro. Wilhelm Roux Arch. Entwickl. Mech. Org. 137(3), 383–403. https://doi.org/10.1007/BF00593068 (1937).
Google Scholar
Seelinger, O. Eibildung und Knospung von Clavelina lepadiformis. Sitzungsber. d. Kais. Kgl. Acad. d. Wiss 1–56 (1882).
Van Beneden, E. & Julin, C. Recherches sur la morphologie des tuniciers. Arch. Biol. 6, 237–476 (1886).
Garstang, W. Memoirs: The morphology of the Tunicata, and its bearings on the phylogeny of the Chordata. J. Cell Sci. 1928(2), 51–187 (1928).
Google Scholar
Kimura, K. D., Tissenbaum, H. A., Liu, Y. X. & Ruvkun, G. daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Science 277, 942–946 (1997).
Google Scholar
Ogawa, A. & Brown, F. Dauer formation and dauer-specific behaviours in Pristionchus pacificus. In Pristionchus pacificus—A nematode model for comparative and evolutionary biology (ed. Sommer, R. J.) (Brill, 2015). https://doi.org/10.1163/9789004260306_011.
Google Scholar
Wisdom, R. AP-1: One switch for many signals. Exp. Cell Res. 253(1), 180–185. https://doi.org/10.1006/excr.1999.4685 (1999).
Google Scholar
Karin, M., Liu, Z. & Zandi, E. AP-1 function and regulation. Curr. Opin. Cell Biol. 9, 240–246 (1997).
Google Scholar
Srivastava, M. Beyond casual resemblances: rigorous frameworks for comparing regeneration across species. Annu. Rev. Cell Dev. Biol. 37, 1–26 (2021).
Google Scholar
Alié, A. et al. Convergent acquisition of nonembryonic development in styelid ascidians. Mol. Biol. Evol. 35, 1728–1743. https://doi.org/10.1093/molbev/msy068 (2018).
Google Scholar
Wang, W., Razy-Krajka, F., Siu, E., Ketcham, A. & Christiaen, L. NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field. PLoS Biol. 11, 1. https://doi.org/10.1371/journal.pbio.1001725 (2013).
Google Scholar
Prünster, M. M., Ricci, L., Brown, F. D. & Tiozzo, S. Modular co-option of cardiopharyngeal genes during non-embryonic myogenesis. EvoDevo https://doi.org/10.1186/s13227-019-0116-7 (2019).
Google Scholar
Kawamura, K., Shiohara, M., Kanda, M. & Fujiwara, S. Retinoid X receptor-mediated transdifferentiation cascade in budding tunicates. Dev. Biol. 384, 343–355 (2013).
Google Scholar
Rinkevich, Y., Paz, G., Rinkevich, B. & Reshef, R. Systemic bud induction and retinoic acid signaling underlie whole body regeneration in the urochordate Botrylloides leachi. PLoS Biol. 5, e71. https://doi.org/10.1371/journal.pbio.0050071 (2007).
Google Scholar
Song, L. & Florea, L. Rcorrector: Efficient and accurate error correction for Illumina RNA-seq reads. GigaScience. 4(1), 48. https://doi.org/10.1186/s13742-015-0089-y (2015).
Google Scholar
Krueger, F. Trim Galore!: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ (2015).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17(1), 10–12. https://doi.org/10.14806/ej.17.1.200 (2011).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9(4), 357–359. https://doi.org/10.1038/nmeth.1923 (2012).
Google Scholar
Andrews, S. FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652. https://doi.org/10.1038/nbt.1883 (2011).
Google Scholar
Laetsch, D. R. & Blaxter, M. L. BlobTools: Interrogation of genome assemblies. F1000Research 6, 1287. https://doi.org/10.12688/f1000research.12232.1 (2017).
Google Scholar
Li, W. & Godzik, A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13), 1658–1659. https://doi.org/10.1093/bioinformatics/btl158 (2006).
Google Scholar
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: Assessing genome assembly and annotation completeness. In Gene prediction (ed. Kollmar, M.) 227–245 (Humana, New York, 2019). https://doi.org/10.1007/978-1-4939-9173-0_14.
Google Scholar
Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368. https://doi.org/10.1038/s41592-021-01101-x (2021).
Google Scholar
The UniProt Consortium. UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Res. 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100 (2021).
Google Scholar
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34(5), 525–527. https://doi.org/10.1038/nbt.3519 (2016).
Google Scholar
Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15(2), 1–17. https://doi.org/10.1186/gb-2014-15-2-r29 (2014).
Google Scholar
Chen, H. & Boutros, P. C. VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform. 12(1), 35. https://doi.org/10.1186/1471-2105-12-35 (2011).
Google Scholar
Kanehisa, M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 28, 1947–1951. https://doi.org/10.1002/pro.3715 (2019).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30. https://doi.org/10.1093/nar/28.1.27 (2000).
Google Scholar
Kanehisa, M., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M. & Tanabe, M. KEGG: Integrating viruses and cellular organisms. Nucleic Acids Res 49(D1), D545–D551. https://doi.org/10.1093/nar/gkaa970 (2021).
Google Scholar
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4(1), 44–57 (2009).
Google Scholar
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37(1), 1–13 (2009).
Google Scholar
Source: Ecology - nature.com
