{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T12:32:17Z","timestamp":1777984337316,"version":"3.51.4"},"reference-count":13,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"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>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. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 64.8 Mb and 76 Mb, respectively.\n                  <\/ns3:p>","DOI":"10.12688\/openreseurope.20666.1","type":"journal-article","created":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T12:35:06Z","timestamp":1754051706000},"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":[[2025,8,1]]},"reference":[{"key":"ref-1","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":"ref-2","article-title":"Species factsheet: Azores Bullfinch Pyrrhula murina","year":"2021"},{"key":"ref-3","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":"ref-4","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-5","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":"A Costa TdMM, Gil","year":"2023","journal-title":"Diversity."},{"key":"ref-11","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.1096.1","article-title":"ERGA-BGE Genome Report ANNOT analyses.","author":"D De Panis","year":"2024a"},{"key":"ref-6","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":"ref-7","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.567.2","article-title":"CLAWS (CNAG\u2019s Long-read Assembly Workflow in Snakemake) [Computer software]","author":"J Gomez-Garrido","year":"2024"},{"key":"ref-8","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":"ref-12","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":"ref-9","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":"ref-13","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":"ref-10","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."}],"updated-by":[{"DOI":"10.12688\/openreseurope.20666.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T00:00:00Z","timestamp":1770768000000}},{"DOI":"10.12688\/openreseurope.20666.3","type":"new_version","label":"New 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with reservations, Approved with reservations","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openreseurope.22356.r57670, Luke W Silver, University of Sydney, Sydney, 28 Aug 2025, version 1, 2 approved with reservations","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v1#referee-response-57670","order":0,"name":"referee-response-57670","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rita Monteiro<\/b>; \n<i>Posted: 29 Jan 2026<\/i>; We thank the reviewer for their comments. We have addressed all of them as following:&nbsp; &nbsp;  Added to the Abstract We included a new figure (Figure 1) that shows the wider spatial context in relation to the nearest continental grounds, and the location of the Azores Bullfinch range inside the S&atilde;o Miguel Island. We also include a photo of the Azores Bullfinch. Modified accordingly. Modified accordingly. Modified accordingly. Were produced 150bp paired end RNA libraries. This information was added to the main text. 91MR were generated, added to the text.  We assembled contigs from ONT data with Hi-C for phasing. We scaffolded with YaHS using Hi-C data. &nbsp;K-mer counts for estimating genome size, QV and k-mer completeness were performed on the combined set of Illumina WGS and filtered ONT reads. This information was added to the text.   For the assembly summary analysis we used BUSCO v5.5.0 and Merqury v1.3. This information was added to the main text.   Yes, repeats were identified using RepeatMasker (Smit, AFA, Hubley, R &amp; Green, P., 2013-2015), (version 4.0.5 with parameters -nolow -engine &quot;RMBlast&quot;), dustmasker (Morgulis, A., et al., 2006), and tandem repeat finder, TRF (Benson, G., 1999). In addition to the Repbase (Bao, W., et al, 2015) library, where available, a custom repeat library is used with RepeatMasker. Custom libraries are created using RepeatModeler2 (Flynn, J.M., 2020)   The mitochondrial genome corresponds to chr OZ239036.1. This was added to the main text.&nbsp;   We have added the following text to the methods: \u201cThe sex chromosomes were identified by sequencing coverage. Assignment of Z and W chromosomes was according to conservation of length: bPyrMur chrZ (OZ238997.1: 86793913 bp) vs. bGalGal chrZ (CM028522.1: 86044486 bp). Whole genome alignment against GRCg7b (GCA_016699485.1) confirmed these assignments.\u201d   As indicated, RNA sequencing was performed for transcriptome profiling with the primary aim of supporting genome assembly and annotation. Although a full genome annotation for this species is not yet available, it is currently being generated and will be released as soon as it becomes available.&nbsp;   We did not include any information with respect to macro- vs. microchromosomes as there is some debate in the literature as to the length threshold (35 Mb? 30? 20 Mb?). It seems that the categorization is done by karytyping and varies from one bird species to the next. For P. murina, the clearest size break occurs between about 23 and 28 Mb. It has 10 autosomes and the Z and W that are longer than 28 Mb and the rest (30 autosomes) are shorter than 23 Mb, the shortest being about 3.5 Mb. &nbsp;We have added this information to the text but avoid the macro- micro- labels.   &nbsp; &nbsp;","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v1#referee-comment-5041","order":1,"name":"referee-comment-5041","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.22356.r57666, Annabel Whibley, University of Auckland, Auckland, 12 Sep 2025, version 1, 2 approved with reservations","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v1#referee-response-57666","order":2,"name":"referee-response-57666","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rita Monteiro<\/b>; \n<i>Posted: 29 Jan 2026<\/i>; We thank the reviewer for their comments. We have addressed all of them as following:   &nbsp;The discrepancy between the previously reported of &nbsp;39 pseudochromosomes (2n=78) &nbsp;and the 42 pseudochromosomes recovered in our assembly can be explained by differences in how the chromosome number was inferred. The number 2n=78 pseudochromosomes was obtained from GOAT, &nbsp;which estimates it based on comparative karyotype data from ancestral taxa (as indicated in the main text) rather than direct cytogenetic observation for this species. We have now modified the text to clarify this point better. In contrast, our assembly provides species specific evidence, revealing 40 pairs of autosomes plus two sex chromosomes. In addition, 11 scaffolds remain unplaced in the current assembly.&nbsp;   As noted in our response to the other reviewer, a full genome annotation for this species is not yet available: it is currently being generated and will be released as soon as completed.&nbsp;   We thank the reviewer for pointing this out. As suggested we have now included the genome size estimation method - GenomeScope2 with a k-mer length of 21. In addition, we have also included the corresponding software versions BUSCO v5.5.0 and Merqury v1.3, as also suggested by the other reviewer. Furthermore, we now report the number and kind of interventions made during manual curation.&nbsp;   We have modified the highlighted examples to improve clarity and formality.   &nbsp;Modified accordingly.   We have clarified the text, separating the RNA-seq data production from the rest of the data, highlighting that the purpose of its &nbsp;production is to aid future annotation efforts. We include transcriptomic data for the purpose of efficiency. Collecting RNA from the same specimen (or from different specimens) during the same sampling event is important and saves time, effort and costs when it comes to annotation of the reference genomes produced. The annotation step is downstream of the assembly and can take substantially more time, thus we release the assemblies as soon as possible and decouple the annotation step from necessary inclusion in the Genome Note.   &nbsp;All relevant metadata, including the collection site and coordinates are are available under the umbrella BioProject PRJEB86373 (https:\/\/www.ebi.ac.uk\/ena\/browser\/view\/PRJEB86373 ) and in the ERGA portal (https:\/\/portal.erga-biodiversity.eu\/data_portal\/928672). Both links are included in the main text.&nbsp; &nbsp;","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-210\/v1#referee-comment-5042","order":3,"name":"referee-comment-5042","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. 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":4,"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"}]}}