{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T14:09:07Z","timestamp":1774879747670,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/openreseurope.21670.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T00:00:00Z","timestamp":1774828800000}}],"reference-count":24,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T00:00:00Z","timestamp":1774828800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018693","name":"Horizon Europe Framework Programme","doi-asserted-by":"publisher","award":["101059492"],"award-info":[{"award-number":["101059492"]}],"id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Agence nationale de la recherche","award":["ANR-10-INBS-09-08"],"award-info":[{"award-number":["ANR-10-INBS-09-08"]}]},{"name":"Spanish Research Agency of the Ministry of Science and Innovation","award":["PID2020-115149GB-C21"],"award-info":[{"award-number":["PID2020-115149GB-C21"]}]},{"name":"Agence nationale de la recherche","award":["ANR-22-EXAT-0003-SEQ-Sea"],"award-info":[{"award-number":["ANR-22-EXAT-0003-SEQ-Sea"]}]},{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["22.00173"],"award-info":[{"award-number":["22.00173"]}]},{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["24.00054"],"award-info":[{"award-number":["24.00054"]}]},{"DOI":"10.13039\/100012818","name":"Autonomous Community of Madrid","doi-asserted-by":"crossref","award":["PIPF-2022\/ECO-24575"],"award-info":[{"award-number":["PIPF-2022\/ECO-24575"]}],"id":[{"id":"10.13039\/100012818","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["open-research-europe.ec.europa.eu"],"crossmark-restriction":false},"short-container-title":["Open Res Europe"],"abstract":"<ns3:p>\n                    The reference genome of\n                    <ns3:italic>Lewinskya acuminata<\/ns3:italic>\n                    (H. Philib.) F. Lara, Garilleti &amp; Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the\n                    <ns3:italic>Orthotrichaceae<\/ns3:italic>\n                    and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, while the mitochondrial and chloroplastic genomes were assembled, respectively, as a single contig of 104,820 bp and two contigs of 123,029 bp and 122,994 bp. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.\n                  <\/ns3:p>","DOI":"10.12688\/openreseurope.21670.2","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T13:19:10Z","timestamp":1774876750000},"page":"357","update-policy":"https:\/\/doi.org\/10.12688\/openreseurope.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["ERGA-BGE reference genome of Lewinskya acuminata, a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia"],"prefix":"10.12688","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8714-9304","authenticated-orcid":false,"given":"Pablo","family":"Aguado-Ramsay","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1665-5277","authenticated-orcid":false,"given":"Francisco","family":"Lara","sequence":"additional","affiliation":[]},{"given":"Isabel","family":"Draper","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1138-7162","authenticated-orcid":false,"given":"Maria","family":"Conejero","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1284-3115","authenticated-orcid":false,"given":"Astrid","family":"B\u00f6hne","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1374-4474","authenticated-orcid":false,"given":"Rita","family":"Monteiro","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1960-9508","authenticated-orcid":false,"given":"Thomas","family":"Marcussen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3280-6239","authenticated-orcid":false,"given":"Torsten","family":"H. Struck","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2094-5592","authenticated-orcid":false,"given":"Rebekah","family":"A. Oomen","sequence":"additional","affiliation":[]},{"name":"Genomescope Sequencing Team","sequence":"additional","affiliation":[]},{"given":"Alice","family":"Moussy","sequence":"additional","affiliation":[]},{"given":"Corinne","family":"Cruaud","sequence":"additional","affiliation":[]},{"given":"Karine","family":"Labadie","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9164-3311","authenticated-orcid":false,"given":"Lola","family":"Demirdjian","sequence":"additional","affiliation":[]},{"given":"Emilie","family":"T\u00e9odori","sequence":"additional","affiliation":[]},{"given":"Patrick","family":"Wincker","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3161-8367","authenticated-orcid":false,"given":"Pedro","family":"H. Oliveira","sequence":"additional","affiliation":[]},{"given":"Jean-Marc","family":"Aury","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6589-6635","authenticated-orcid":false,"given":"Chiara","family":"Bortoluzzi","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2026,3,30]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"979-992","DOI":"10.1111\/jse.13040","article-title":"Seeking the identity of an enigmatic moss by embracing phylogenomics.","volume":"62","author":"P Aguado-Ramsay","year":"2024","journal-title":"J Syst Evol."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"186-188","DOI":"10.1080\/03736687.2019.1655871","article-title":"Earliest herbarium evidence for the occurrence of Lewinskya acuminata (Orthotrichaceae) in East Africa.","volume":"42","author":"J Calleja","year":"2020","journal-title":"J Bryol."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"24","DOI":"10.12688\/wellcomeopenres.18658.1","article-title":"Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved].","volume":"8","author":"R Challis","year":"2023","journal-title":"Wellcome Open Res."},{"key":"ref-32","doi-asserted-by":"publisher","first-page":"2896-2898","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies.","volume":"36","author":"D Guan","year":"2020","journal-title":"Bioinformatics."},{"key":"ref-4","article-title":"PretextView (Paired REad TEXTure Viewer): a desktop application for viewing pretext contact maps","author":"E Harry","year":"2022"},{"key":"ref-5","article-title":"Checklist and country status of European bryophytes\u2013update 2020","author":"N Hodgetts","year":"2020"},{"key":"ref-6","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03252-4","article-title":"NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads.","volume":"25","author":"J Hu","year":"2024","journal-title":"Genome Biol."},{"key":"ref-9","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2024.1451005","article-title":"Unveiling the diversification and dispersal of the Lewinskya firma complex (Orthotrichaceae, Bryophyta) across Africa and India.","volume":"15","author":"F Lara","year":"2024","journal-title":"Front Plant Sci."},{"key":"ref-7","first-page":"50-135","article-title":"Orthotrichum","volume":"2014","author":"F Lara","year":"2014"},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"361-382","DOI":"10.7872\/cryb\/v37.iss4.2016.361","article-title":"Lewinskya, a new genus to accommodate the phaneroporous and monoicous taxa of Orthotrichum (Bryophyta, Orthotrichaceae).","volume":"37","author":"F Lara","year":"2016","journal-title":"Cryptogam Bryol."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"1-13","DOI":"10.1080\/03736687.2025.2548733","article-title":"Lewinskya crinita sp. nov. and L. aristoblephara comb. nov. 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Ascertaining a new case of intercontinental disjunction in mosses.","volume":"180","author":"B Vigalondo","year":"2016","journal-title":"Bot J Linn Soc."},{"key":"ref-33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03676-6","article-title":"Oatk: a de novo assembly tool for complex plant organelle genomes.","volume":"26","author":"C Zhou","year":"2025","journal-title":"Genome Biol."},{"key":"ref-31","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: Yet another Hi-C Scaffolding tool.","volume":"39","author":"C Zhou","year":"2023","journal-title":"Bioinformatics."}],"container-title":["Open Research Europe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T13:19:12Z","timestamp":1774876752000},"score":1,"resource":{"primary":{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,30]]},"references-count":24,"URL":"https:\/\/doi.org\/10.12688\/openreseurope.21670.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/openreseurope.21670.1","asserted-by":"subject"}]},"ISSN":["2732-5121"],"issn-type":[{"value":"2732-5121","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,30]]},"assertion":[{"value":"Indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openreseurope.23442.r65418, Qilin Yang, University of Chinese Academy of Sciences, Beijing, 02 Jan 2026, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v1#referee-response-65418","order":0,"name":"referee-response-65418","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 27 Jan 2026<\/i>; We thank the reviewer for their comments and for their kind words. We have addressed all points as follow:&nbsp; 1. We have now corrected the 'Genetic information' section as suggested. 2. We have changed the abstract to match what reported in the 'Methods' section to avoid any further confusion. 3. We thank the reviewer for point out the issue with the BUSCO lineage. We have now corrected this in the 'Results' section to provide more context. 4. We have now corrected Figure 1.&nbsp; 5. All typos have been corrected.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2#referee-comment-5037","order":1,"name":"referee-comment-5037","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 30 Jan 2026<\/i>; We thank the reviewer for their comments. We have addressed all comments as follow:  We now corrected the \u2018Genetic information\u2019 section as suggested. We changed the abstract to match what reported in the Methods section to avoid any further confusion. We have corrected the BUSCO score in the Results section.&nbsp; We have now corrected Figure 1. We have corrected all typos.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2#referee-comment-5046","order":2,"name":"referee-comment-5046","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.23442.r67500, Panagiotis Ioannidis, Foundation for Research & Technology- Hellas, Crete, 20 Jan 2026, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v1#referee-response-67500","order":3,"name":"referee-response-67500","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 27 Jan 2026<\/i>; We thank the reviewer for their comments and suggestions. All comments have been addressed as follow:  As also pointed out by Reviewer 1, the 'low' BUSCO completeness score is due to a bias in the&nbsp;embryophyta database used in the BUSCO analysis. We described this bias in the 'Results' section. Yes, the genome annotation will be available through the Ensembl website and it will make use of the RNA-Seq data generated along with the genome assembly. All these additional QC are already reported in the ERGA Assembly Report (or EAR) which accompanies this Genome Report, as reported in the Methods section (https:\/\/github.com\/ERGA-consortium\/EARs\/blob\/main\/Assembly_Reports\/Lewinskya_acuminata\/cbLewAcum8\/cbLewAcum8.1_EAR.pdf).&nbsp; As before, all these additional information are already reported in the EAR (https:\/\/github.com\/ERGA-consortium\/EARs\/blob\/main\/Assembly_Reports\/Lewinskya_acuminata\/cbLewAcum8\/cbLewAcum8.1_EAR.pdf).&nbsp; We added a table showing the lenghts (and accessions) of the chromosome-level assembly.&nbsp; We added a Figure showing the blob plot results.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2#referee-comment-5038","order":4,"name":"referee-comment-5038","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 30 Jan 2026<\/i>; We thank the reviewer for their feedback. We have addressed all commens as follow:  As also pointed out by Reviewer 1, the \u2018low\u2019 BUSCO completeness score is due to a bias in the embryophyta database used in the BUSCO analysis. We described this bias in the Results section. Yes, the genome annotation will be available through the Ensembl website and it will make use of the RNA-Seq data generated along with the genome assembly. All these additional QC are already reported in the ERGA Assembly Report (or EAR) which accompanies this Genome Report, as reported in the Methods section (https:\/\/github.com\/ERGA-consortium\/EARs\/blob\/main\/Assembly_Reports\/Lewinskya_acuminata\/cbLewAcum8\/cbLewAcum8.1_EAR.pdf). We added an additional table to the Report with information on the chromosomes and their length. We now added a new Figure (blobl plot) to address this comment.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2#referee-comment-5047","order":5,"name":"referee-comment-5047","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.23442.r67496, Annabel Whibley, Grapevine Improvement, Bragato Research Institute, Lincoln, 04 Feb 2026, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v1#referee-response-67496","order":6,"name":"referee-response-67496","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 05 Feb 2026<\/i>; We thank the reviewer for their comment. We addressed all comments as follow:&nbsp;  Also pointed out by the other reviewers, we now clarified in the main text why the BUSCO completeness score is relatively low. Briefly, the high missing score is often elevated when using the embryophyta_odb10 lineage set in bryophytes, as the lineage is biased towards vascular plants. We have expanded the presentation of the results, as also suggested by another reviewer. The Report now has an additional Table on the set of chromosomes and their length and an additional figure (blob plot). No verification of species via DNA barcode was performed.&nbsp; Most of the information requested by the reviewer (k-mer, heterozygosity, etc) is already reported in the ERGA Assembly Report or EAR, which is reported in the main text already. RNA was extracted, but the annotation is not provided because is undergoing. As also suggested by another reviewer, we now corrected the confusion associated with the number of chromosomes.&nbsp;&nbsp;","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-357\/v2#referee-comment-5064","order":7,"name":"referee-comment-5064","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Biodiversity Genomics Europe (Grant no.101059492) is funded by Horizon Europe under the Biodiversity, Circular Economy and Environment call (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract numbers 22.00173 and 24.00054; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy\u2019s Horizon Europe Guarantee Scheme. Pablo Aguado-Ramsay, Francisco Lara, and Isabel Draper have received funding by the Spanish Research Agency of the Ministry of Science and Innovation (grant PID2020-115149GB-C21). Pablo Aguado-Ramsay has financial support from the Autonomous Community of Madrid (PIPF-2022\/ECO-24575). This work was supported by the Genoscope, the Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives (CEA), France G\u00e9nomique (ANR-10-INBS-09-08), and the exploratory research programme \u2018ATLASea: Atlas of marine genomes and its targeted project SEQ-Sea (ANR-22-EXAT-0003-SEQ-Sea). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":8,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}