{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T12:33:24Z","timestamp":1777984404390,"version":"3.51.4"},"update-to":[{"DOI":"10.12688\/openreseurope.20666.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T00:00:00Z","timestamp":1773187200000}},{"DOI":"10.12688\/openreseurope.20666.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T00:00:00Z","timestamp":1773187200000}}],"reference-count":13,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T00:00:00Z","timestamp":1773187200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["open-research-europe.ec.europa.eu"],"crossmark-restriction":false},"short-container-title":["Open Res Europe"],"abstract":"<ns3:p>\n                    <ns3:italic>The reference genome of Pyrrhula murina<\/ns3:italic>\n                    \u2019s reference genome will substantially enhance the current monitoring of genetic diversity and population viability and will allow us to understand the effective population size trends throughout time and recent bottlenecks and population expansions. A total of 42 contiguous chromosomal pseudomolecules were assembled from the genome sequence, using ONT, HI-C and Illumina data. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 65 Mb and 76 Mb, respectively.\n                  <\/ns3:p>","DOI":"10.12688\/openreseurope.20666.3","type":"journal-article","created":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T16:24:10Z","timestamp":1773246250000},"page":"210","update-policy":"https:\/\/doi.org\/10.12688\/openreseurope.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["ERGA-BGE reference genome of the Azores Bullfinch - Pyrrhula murina Godman, 1866: an IUCN Vulnerable Species endemic to a single island in the Azores Archipelago (Portugal)"],"prefix":"10.12688","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2193-5107","authenticated-orcid":false,"given":"Ricardo Jorge","family":"Lopes","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1284-3115","authenticated-orcid":false,"given":"Astrid","family":"B\u00f6hne","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1960-9508","authenticated-orcid":false,"given":"Thomas","family":"Marcussen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2094-5592","authenticated-orcid":false,"given":"Rebekah A.","family":"Oomen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3280-6239","authenticated-orcid":false,"given":"Torsten Hugo","family":"Struck","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8631-8778","authenticated-orcid":false,"given":"Laura","family":"Aguilera","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4063-7159","authenticated-orcid":false,"given":"Marta","family":"Gut","sequence":"additional","affiliation":[]},{"given":"Francisco","family":"C\u00e2mara Ferreira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4098-8829","authenticated-orcid":false,"given":"Fernando","family":"Cruz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6409-8009","authenticated-orcid":false,"given":"J\u00e8ssica","family":"G\u00f3mez-Garrido","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2960-5420","authenticated-orcid":false,"given":"Tyler S.","family":"Alioto","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1374-4474","authenticated-orcid":false,"given":"Rita","family":"Monteiro","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2026,3,11]]},"reference":[{"key":"ref1","first-page":"23-62","article-title":"The Azores Bullfinch - Pyrrhula murina GODMAN, 1866 The history of a bird species: persecuted - missing - rediscovered - protected (?) (including a list of all known specimens and syntypes).","volume":"102","author":"G Aubrecht","year":"2000","journal-title":"Ann Nat Mus Wien."},{"key":"ref2","article-title":"Species factsheet: Azores Bullfinch Pyrrhula murina.","year":"2021"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"477-489","DOI":"10.1017\/S0959270911000025","article-title":"Status assessment of the critically endangered Azores Bullfinch Pyrrhula murina.","volume":"21","author":"R Ceia","year":"2011","journal-title":"Bird Conserv Int."},{"key":"ref4","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":"ref5","doi-asserted-by":"publisher","first-page":"685","DOI":"10.3390\/d15050685","article-title":"How many Azores Bullfinches (Pyrrhula murina) are there in the world? case study of a threatened species.","volume":"15","author":"T Costa","year":"2023","journal-title":"Diversity."},{"key":"ref6","article-title":"ASM analyses (one-asm WGS Illumina PE + HiC).","author":"D De Panis","year":"2024","journal-title":"WorkflowHub."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"45-52","DOI":"10.1016\/j.ecoleng.2015.10.028","article-title":"The Priolo Atlas: a citizen science-based census initiative for supporting Pyrrhula murina habitat conservation and restoration policies in S\u00e3o Miguel Island (Azores, Portugal).","volume":"86","author":"A Gil","year":"2016","journal-title":"Ecol Eng."},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.567.2","author":"J Gomez-Garrido","year":"2024","journal-title":"CLAWS (CNAG\u2019s Long-read Assembly Workflow in Snakemake) [Computer software]."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"677-687","DOI":"10.1111\/j.1095-8312.2012.02040.x","article-title":"The Azores bullfinch (Pyrrhula murina) has the same unusual and size-variable sperm morphology as the Eurasian bullfinch (Pyrrhula pyrrhula).","volume":"108","author":"J Lifjeld","year":"2013","journal-title":"Biol J Linn Soc."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"e323","DOI":"10.1002\/cpz1.323","article-title":"BUSCO: assessing genomic data quality and beyond.","volume":"1","author":"M Manni","year":"2021","journal-title":"Curr Protoc."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/d41586-023-02229-w","article-title":"Biodiversity: an Atlas of European reference genomes.","volume":"619","author":"C Mazzoni","year":"2023","journal-title":"Nature."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.","volume":"21","author":"A Rhie","year":"2020","journal-title":"Genome Biol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"271-282","DOI":"10.1016\/j.ympev.2010.10.015","article-title":"A molecular phylogeny of bullfinches Pyrrhula Brisson, 1760 (Aves: Fringillidae).","volume":"58","author":"T T\u00f6pfer","year":"2011","journal-title":"Mol Phylogenet Evol."}],"container-title":["Open Research Europe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T09:04:08Z","timestamp":1773306248000},"score":1,"resource":{"primary":{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,11]]},"references-count":13,"URL":"https:\/\/doi.org\/10.12688\/openreseurope.20666.3","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/openreseurope.20666.2","asserted-by":"subject"},{"id-type":"doi","id":"10.12688\/openreseurope.20666.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.21956\/openreseurope.25295.r71045","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/openreseurope.25295.r71044","asserted-by":"object"}]},"ISSN":["2732-5121"],"issn-type":[{"value":"2732-5121","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,11]]},"assertion":[{"value":"Indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openreseurope.24922.r69517, Luke W Silver, University of Sydney, Sydney, 27 Feb 2026, version 2, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v2#referee-response-69517","order":0,"name":"referee-response-69517","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rita Monteiro<\/b>; \n<i>Posted: 05 Mar 2026<\/i>; We thank the reviewer for this suggestion. However, ERGA-BGE genome reports are specifically scoped to present the assembly and its core metrics, rather than provide detailed genomic analyses. Additionally, including a full repeat breakdown could conflict with more in-depth work being carried out by the sample provider for future publications. We have therefore respectfully maintained the current level of detail in this section.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3#referee-comment-5112","order":1,"name":"referee-comment-5112","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.24922.r69516, Annabel Whibley, University of Auckland, Auckland, 27 Feb 2026, version 2, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v2#referee-response-69516","order":2,"name":"referee-response-69516","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rita Monteiro<\/b>; \n<i>Posted: 05 Mar 2026<\/i>; We thank the reviewer for these suggestions. 1.Corrected&nbsp; 2.&nbsp;Added to the main text: Basecalling was performed using Dorado v7.4.14 (Oxford nanopore Technologies) with the super accurate (SUP) basecalling model v4.3.0 at 400 bps, integrated within MinKNOW v24.06.15.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v3#referee-comment-5113","order":3,"name":"referee-comment-5113","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.24922.r69658, Madeline Chase, Swiss Ornithological Institute, Sempach, 12 Mar 2026, version 2, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v2#referee-response-69658","order":4,"name":"referee-response-69658","label":"Referee Report","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. RJL was funded by the grant UID\/00329\/2025 awarded to Centro de Ecologia, Evolu\u00e7\u00e3o e Altera\u00e7\u00f5es Ambientais (CE3C). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"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"}]}}