{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T06:06:56Z","timestamp":1782540416505,"version":"3.54.5"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"7690","license":[{"start":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T00:00:00Z","timestamp":1516752000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T00:00:00Z","timestamp":1516752000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>The planarian <jats:italic>Schmidtea mediterranea<\/jats:italic> is an important model for stem cell research and regeneration, but adequate genome resources for this species have been lacking. Here we report a highly contiguous genome assembly of <jats:italic>S. mediterranea<\/jats:italic>, using long-read sequencing and a <jats:italic>de novo<\/jats:italic> assembler (MARVEL) enhanced for low-complexity reads. The <jats:italic>S. mediterranea<\/jats:italic> genome is highly polymorphic and repetitive, and harbours a novel class of giant retroelements. Furthermore, the genome assembly lacks a number of highly conserved genes, including critical components of the mitotic spindle assembly checkpoint, but planarians maintain checkpoint function. Our genome assembly provides a key model system resource that will be useful for studying regeneration and the evolutionary plasticity of core cell biological mechanisms.<\/jats:p>","DOI":"10.1038\/nature25473","type":"journal-article","created":{"date-parts":[[2018,1,30]],"date-time":"2018-01-30T17:31:16Z","timestamp":1517333476000},"page":"56-61","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":232,"title":["The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms"],"prefix":"10.1038","volume":"554","author":[{"given":"Markus Alexander","family":"Grohme","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siegfried","family":"Schloissnig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrei","family":"Rozanski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Pippel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George Robert","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylke","family":"Winkler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holger","family":"Brandl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Henry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Dahl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Powell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hiller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene","family":"Myers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jochen Christian","family":"Rink","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,1,24]]},"reference":[{"key":"BFnature25473_CR1","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1007\/s00427-012-0426-4","volume":"223","author":"JC Rink","year":"2013","unstructured":"Rink, J. C. Stem cell systems and regeneration in planaria. Dev. Genes Evol. 223, 67\u201384 (2013)","journal-title":"Dev. Genes Evol."},{"key":"BFnature25473_CR2","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1387\/ijdb.123495es","volume":"56","author":"E Sal\u00f3","year":"2012","unstructured":"Sal\u00f3, E. & Agata, K. Planarian regeneration: a classic topic claiming new attention. Int. J. Dev. Biol. 56, 3\u20134 (2012)","journal-title":"Int. J. Dev. Biol."},{"key":"BFnature25473_CR3","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1146\/annurev.cellbio.20.010403.095114","volume":"20","author":"PW Reddien","year":"2004","unstructured":"Reddien, P. W. & S\u00e1nchez Alvarado, A. Fundamentals of planarian regeneration. Annu. Rev. Cell Dev. Biol. 20, 725\u2013757 (2004)","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"BFnature25473_CR4","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1126\/science.1203983","volume":"332","author":"DE Wagner","year":"2011","unstructured":"Wagner, D. E., Wang, I. E. & Reddien, P. W. Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science 332, 811\u2013816 (2011)","journal-title":"Science"},{"key":"BFnature25473_CR5","doi-asserted-by":"publisher","first-page":"2755","DOI":"10.1038\/emboj.2012.110","volume":"31","author":"P Onal","year":"2012","unstructured":"Onal, P. et al. Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. EMBO J. 31, 2755\u20132769 (2012)","journal-title":"EMBO J."},{"key":"BFnature25473_CR6","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature12031","volume":"496","author":"IJ Tsai","year":"2013","unstructured":"Tsai, I. J. et al. The genomes of four tapeworm species reveal adaptations to parasitism. Nature 496, 57\u201363 (2013)","journal-title":"Nature"},{"key":"BFnature25473_CR7","doi-asserted-by":"publisher","first-page":"e05503","DOI":"10.7554\/eLife.05503","volume":"4","author":"CE Laumer","year":"2015","unstructured":"Laumer, C. E., Hejnol, A. & Giribet, G. Nuclear genomic signals of the \u2018microturbellarian\u2019 roots of platyhelminth evolutionary innovation. eLife 4, e05503 (2015)","journal-title":"eLife"},{"key":"BFnature25473_CR8","doi-asserted-by":"publisher","first-page":"e1003396","DOI":"10.1371\/journal.ppat.1003396","volume":"9","author":"JJ Collins III","year":"2013","unstructured":"Collins, J. J., III & Newmark, P. A. It\u2019s no fluke: the planarian as a model for understanding schistosomes. PLoS Pathog. 9, e1003396 (2013)","journal-title":"PLoS Pathog."},{"key":"BFnature25473_CR9","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1101\/gr.6743907","volume":"18","author":"BL Cantarel","year":"2008","unstructured":"Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188\u2013196 (2008)","journal-title":"Genome Res."},{"key":"BFnature25473_CR10","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1002\/dvg.22872","volume":"53","author":"SMC Robb","year":"2015","unstructured":"Robb, S. M. C., Gotting, K., Ross, E. & S\u00e1nchez Alvarado, A. SmedGD 2.0: The Schmidtea mediterranea genome database. Genesis 53, 535\u2013546 (2015)","journal-title":"Genesis"},{"key":"BFnature25473_CR11","doi-asserted-by":"publisher","first-page":"e0143525","DOI":"10.1371\/journal.pone.0143525","volume":"10","author":"O Nishimura","year":"2015","unstructured":"Nishimura, O. et al. Unusually large number of mutations in asexually reproducing clonal planarian Dugesia japonica. PLoS One 10, e0143525 (2015)","journal-title":"PLoS One"},{"key":"BFnature25473_CR12","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1126\/science.1162986","volume":"323","author":"J Eid","year":"2009","unstructured":"Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133\u2013138 (2009)","journal-title":"Science"},{"key":"BFnature25473_CR13","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.15252\/embr.201744102","volume":"18","author":"JJ van Hooff","year":"2017","unstructured":"van Hooff, J. J., Tromer, E., van Wijk, L. M., Snel, B. & Kops, G. J. Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics. EMBO Rep. 18, 1559\u20131571 (2017)","journal-title":"EMBO Rep."},{"key":"BFnature25473_CR14","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nrm2163","volume":"8","author":"A Musacchio","year":"2007","unstructured":"Musacchio, A. & Salmon, E. D. The spindle-assembly checkpoint in space and time. Nat. Rev. Mol. Cell Biol. 8, 379\u2013393 (2007)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"BFnature25473_CR15","doi-asserted-by":"publisher","unstructured":"Nowoshilow, S. et al. The axolotl genome and the evolution of key tissue formation regulators. Nature \n                    https:\/\/doi.org\/10.1038\/nature25458\n                    \n                   (2018)","DOI":"10.1038\/nature25458"},{"key":"BFnature25473_CR16","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722\u2013736 (2017)","journal-title":"Genome Res."},{"key":"BFnature25473_CR17","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1101\/gr.193474.115","volume":"26","author":"NH Putnam","year":"2016","unstructured":"Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342\u2013350 (2016)","journal-title":"Genome Res."},{"key":"BFnature25473_CR18","doi-asserted-by":"publisher","first-page":"D764","DOI":"10.1093\/nar\/gkv1148","volume":"44","author":"H Brandl","year":"2016","unstructured":"Brandl, H. et al. PlanMine\u2014a mineable resource of planarian biology and biodiversity. Nucleic Acids Res. 44, D764\u2013D773 (2016)","journal-title":"Nucleic Acids Res."},{"key":"BFnature25473_CR19","doi-asserted-by":"crossref","unstructured":"Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520\u2013562 (2002)","DOI":"10.1038\/nature01262"},{"key":"BFnature25473_CR20","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.gene.2006.08.007","volume":"390","author":"J Macas","year":"2007","unstructured":"Macas, J. & Neumann, P. Ogre elements\u2014a distinct group of plant Ty3\/gypsy-like retrotransposons. Gene 390, 108\u2013116 (2007)","journal-title":"Gene"},{"key":"BFnature25473_CR21","doi-asserted-by":"publisher","first-page":"0019","DOI":"10.1038\/s41559-016-0019","volume":"1","author":"L Guo","year":"2016","unstructured":"Guo, L., Zhang, S., Rubinstein, B., Ross, E. & Alvarado, A. S. Widespread maintenance of genome heterozygosity in Schmidtea?mediterranea. Nat. Ecol. Evol. 1, 0019 (2016)","journal-title":"Nat. Ecol. Evol."},{"key":"BFnature25473_CR22","doi-asserted-by":"publisher","first-page":"12462","DOI":"10.1073\/pnas.1516718112","volume":"112","author":"K Wasik","year":"2015","unstructured":"Wasik, K. et al. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc. Natl Acad. Sci. USA 112, 12462\u201312467 (2015)","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnature25473_CR23","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1016\/j.ydbio.2017.07.023","volume":"433","author":"AG Lai","year":"2018","unstructured":"Lai, A. G., Kosaka, N., Abnave, P., Sahu, S. & Aboobaker, A. A. The abrogation of condensin function provides independent evidence for defining the self-renewing population of pluripotent stem cells. Dev. Biol. 433, 218\u2013226 (2018)","journal-title":"Dev. Biol."},{"key":"BFnature25473_CR24","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/j.tcb.2015.07.009","volume":"26","author":"R Ceccaldi","year":"2016","unstructured":"Ceccaldi, R., Rondinelli, B. & D\u2019Andrea, A. D. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 26, 52\u201364 (2016)","journal-title":"Trends Cell Biol."},{"key":"BFnature25473_CR25","doi-asserted-by":"publisher","first-page":"e14175","DOI":"10.7554\/eLife.14175","volume":"5","author":"BM Stubenhaus","year":"2016","unstructured":"Stubenhaus, B. M. et al. Light-induced depigmentation in planarians models the pathophysiology of acute porphyrias. eLife 5, e14175 (2016)","journal-title":"eLife"},{"key":"BFnature25473_CR26","doi-asserted-by":"publisher","first-page":"4270","DOI":"10.1073\/pnas.0500877102","volume":"102","author":"AU Rao","year":"2005","unstructured":"Rao, A. U., Carta, L. K., Lesuisse, E. & Hamza, I. Lack of heme synthesis in a free-living eukaryote. Proc. Natl Acad. Sci. USA 102, 4270\u20134275 (2005)","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnature25473_CR27","doi-asserted-by":"publisher","first-page":"e20607","DOI":"10.7554\/eLife.20607","volume":"5","author":"M Grudniewska","year":"2016","unstructured":"Grudniewska, M. et al. Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano. eLife 5, e20607 (2016)","journal-title":"eLife"},{"key":"BFnature25473_CR28","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/nrm4025","volume":"16","author":"S Santaguida","year":"2015","unstructured":"Santaguida, S. & Amon, A. Short- and long-term effects of chromosome mis-segregation and aneuploidy. Nat. Rev. Mol. Cell Biol. 16, 473\u2013485 (2015)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"BFnature25473_CR29","doi-asserted-by":"publisher","first-page":"371","DOI":"10.2307\/1539130","volume":"112","author":"MA McWhinnie","year":"1957","unstructured":"McWhinnie, M. A. & Gleason, M. M. Histological changes in regenerating pieces of Dugesia dorotocephala treated with colchicine. Biol. Bull. 112, 371\u2013376 (1957)","journal-title":"Biol. Bull."},{"key":"BFnature25473_CR30","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1002\/dvdy.21928","volume":"238","author":"H Kang","year":"2009","unstructured":"Kang, H. & S\u00e1nchez Alvarado, A. Flow cytometry methods for the study of cell-cycle parameters of planarian stem cells. Dev. Dyn. 238, 1111\u20131117 (2009)","journal-title":"Dev. Dyn."},{"key":"BFnature25473_CR31","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1016\/j.devcel.2015.11.012","volume":"35","author":"V Sili\u00f3","year":"2015","unstructured":"Sili\u00f3, V., McAinsh, A. D. & Millar, J. B. KNL1-Bubs and RZZ provide two separable pathways for checkpoint activation at human kinetochores. Dev. Cell 35, 600\u2013613 (2015)","journal-title":"Dev. Cell"},{"key":"BFnature25473_CR32","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1534\/genetics.116.186759","volume":"205","author":"J Sekelsky","year":"2017","unstructured":"Sekelsky, J. DNA repair in Drosophila: mutagens, models, and missing genes. Genetics 205, 471\u2013490 (2017)","journal-title":"Genetics"},{"key":"BFnature25473_CR33","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1016\/j.cell.2008.09.039","volume":"135","author":"G Rancati","year":"2008","unstructured":"Rancati, G. et al. Aneuploidy underlies rapid adaptive evolution of yeast cells deprived of a conserved cytokinesis motor. Cell 135, 879\u2013893 (2008)","journal-title":"Cell"},{"key":"BFnature25473_CR34","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1007\/s10750-007-9002-8","volume":"595","author":"ER Schockaert","year":"2008","unstructured":"Schockaert, E. R. et al. Global diversity of free living flatworms (Platyhelminthes, \u2018Turbellaria\u2019) in freshwater. Hydrobiologia 595, 41\u201348 (2008)","journal-title":"Hydrobiologia"},{"key":"BFnature25473_CR35","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1016\/j.devcel.2015.11.004","volume":"35","author":"O Wurtzel","year":"2015","unstructured":"Wurtzel, O. et al. A generic and cell-type-specific wound response precedes regeneration in planarians. Dev. Cell 35, 632\u2013645 (2015)","journal-title":"Dev. Cell"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nature25473.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nature25473","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/doifinder\/10.1038\/nature25473","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/www.nature.com\/articles\/nature25473.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T18:11:43Z","timestamp":1684433503000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nature25473"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,24]]},"references-count":35,"journal-issue":{"issue":"7690","published-print":{"date-parts":[[2018,2,1]]}},"alternative-id":["BFnature25473"],"URL":"https:\/\/doi.org\/10.1038\/nature25473","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,24]]},"assertion":[{"value":"6 April 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 December 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}