{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:41:58Z","timestamp":1786977718165,"version":"build-2736575974"},"reference-count":52,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2025,4,25]],"date-time":"2025-04-25T00:00:00Z","timestamp":1745539200000},"content-version":"vor","delay-in-days":24,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100001275","name":"Oak Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001275","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012525","name":"Galapagos Conservancy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012525","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Ecology and Evolution"],"published-print":{"date-parts":[[2025,4]]},"abstract":"ABSTRACT<\/jats:title>\n \n The utility and importance of whole\u2010genome sequences are recognized across various fields, including evolution and conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high\u2010quality DNA is impossible. In such cases, an alternative may be to employ synteny\u2010based methods using a genome from a closely related taxon to generate more complete genomes. Here we update the reference genome for the Pinta Island Galapagos giant tortoise (\n \n Chelonoidis abingdonii<\/jats:italic>\n <\/jats:styled-content>\n ) without conducting additional sequencing through rescaffolding against the most closely related chromosome\u2010level genome assembly, the Aldabra giant tortoise (\n \n Aldabrachelys gigantea<\/jats:italic>\n <\/jats:styled-content>\n ). This effort resulted in a much more contiguous genome, CheloAbing_2.0, with an N50 that is two orders of magnitude longer and large reductions in L50 and the number of gaps. We then examined the impact of the CheloAbing_2.0 genome on estimates of runs of homozygosity (ROH) using genome resequencing data from 37 individual Galapagos giant tortoises from the 13 extant lineages to test the mechanisms by which a fragmented assembly may over\u2010 or underestimate the number and extent of ROH. The use of CheloAbing_2.0 resulted in individual estimates of inbreeding, including ROH proportion (F\n ROH<\/jats:sub>\n ), number (N\n ROH<\/jats:sub>\n ), and cumulative length (S\n ROH<\/jats:sub>\n ), that were statistically different from those derived from the earlier genome assembly. This improved genome will serve as a resource for future efforts focusing on the ecology, evolution, and conservation of this species group. More broadly, our results highlight that synteny\u2010based scaffolding is promising for generating contiguous genomes without needing additional data types.\n <\/jats:p>","DOI":"10.1002\/ece3.71358","type":"journal-article","created":{"date-parts":[[2025,4,26]],"date-time":"2025-04-26T01:56:11Z","timestamp":1745632571000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity"],"prefix":"10.1002","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1819-3117","authenticated-orcid":false,"given":"Evelyn L.","family":"Jensen","sequence":"first","affiliation":[{"name":"School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiara","family":"Marchisio","sequence":"additional","affiliation":[{"name":"School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne UK"},{"name":"Faculty of Health and Life Sciences Universitat Pompeu Fabra Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3271-3684","authenticated-orcid":false,"given":"Alexander","family":"Ochoa","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1192-1505","authenticated-orcid":false,"given":"Rachel","family":"Gray","sequence":"additional","affiliation":[{"name":"School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Parra","sequence":"additional","affiliation":[{"name":"Biology Department University of Kentucky Lexington Kentucky USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4019-7675","authenticated-orcid":false,"given":"Joshua M.","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences MacEwan University Edmonton Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4575-1487","authenticated-orcid":false,"given":"F. G\u00f6zde","family":"\u00c7ilingir","sequence":"additional","affiliation":[{"name":"Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland"},{"name":"Swiss Federal Institute for Research WSL Birmensdorf Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adalgisa","family":"Caccone","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,4,25]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr174"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2012.05.001"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.13167"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/est084"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes10110846"},{"key":"e_1_2_9_8_1","volume-title":"Picard Toolkit","author":"Broad Institute","year":"2019"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592-018-1099-y"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.0014\u20103820.2002.tb00131.x"},{"key":"e_1_2_9_11_1","unstructured":"Cayot L. J. J. P.Gibbs W.Tapia andA.Caccone.2017.\u201cChelonoidis donfaustoi.\u201dThe IUCN Red List of Threatened Species:e.T90377132A90377135."},{"key":"e_1_2_9_12_1","unstructured":"Cayot L. J. J. P.Gibbs W.Tapia andA.Caccone.2022.\u201cChelonoidis darwini(Amended Version of 2016 Assessment).\u201dThe IUCN Red List of Threatened Species:e.T9020A217759496."},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2017.109"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giac090"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes9020072"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac048"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1921046117"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2021.11.008"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/evolut\/qpae164"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esp086"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2109019118"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1111\/eva.12682"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-03483-w"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.16176"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1220349110"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1720115115"},{"key":"e_1_2_9_30_1","unstructured":"Li H.2013.\u201cAligning Sequence Reads Clone Sequences and Assembly Contigs With BWA\u2010MEM.\u201darXiv."},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab199"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-6463-x"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0303408"},{"key":"e_1_2_9_34_1","unstructured":"NCBI.2023.\u201cForeign Contamination Screen.\u201dhttps:\/\/github.com\/ncbi\/fcs."},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv566"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abm8127"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0663-4"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13457"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1086\/519795"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-018-0733-x"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010021\u201003451\u20100"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.3854\/crm.5"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010019\u201012741\u20101"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2014.063"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13104-016-1900-2"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-9525(01)02484-2"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1016"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa063"},{"key":"e_1_2_9_49_1","unstructured":"Smit A. 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