{"doi":"10.1016/j.celrep.2023.111992","title":"A chromosome-level reference genome and pangenome for barn swallow population genomics","abstract":"Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.","journal":"Cell Reports","year":2023,"id":324527,"datarank":0.8208545356039557,"base_score":3.5263605246161616,"endowment":3.5263605246161616,"self_citation_contribution":0.5289540786924243,"citation_network_contribution":0.29190045691153144,"self_endowment_contribution":0.5289540786924243,"citer_contribution":0.29190045691153144,"corpus_percentile":75.42353214202831,"corpus_rank":3178,"citation_count":33,"citer_count":23,"citers_with_citation_signal":18,"citers_with_endowment":18,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9328,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":79.1667,"fair_percentile":97.67655151329869,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":991931,"name":"Guido Roberto Gallo","orcid":"0000-0001-5980-0326","position":1,"is_corresponding":false},{"id":991932,"name":"Marcella Sozzoni","orcid":"0009-0007-6170-7295","position":2,"is_corresponding":false},{"id":991933,"name":"Alessio Iannucci","orcid":"0000-0001-7729-4412","position":3,"is_corresponding":false},{"id":992247,"name":"Elena Galati","orcid":null,"position":4,"is_corresponding":false},{"id":991934,"name":"Linelle Abueg","orcid":"0000-0002-6879-3954","position":5,"is_corresponding":false},{"id":21328,"name":"Jennifer Balacco","orcid":"0000-0001-7102-1632","position":6,"is_corresponding":false},{"id":992248,"name":"Manuela Caprioli","orcid":null,"position":7,"is_corresponding":false},{"id":2108,"name":"William Chow","orcid":"0000-0002-9056-201X","position":8,"is_corresponding":false},{"id":24578,"name":"Claúdio Ciofi","orcid":"0000-0001-8537-8659","position":9,"is_corresponding":false},{"id":2109,"name":"Joanna Collins","orcid":"0000-0001-5782-5028","position":10,"is_corresponding":false},{"id":30838,"name":"Olivier Fédrigo","orcid":"0000-0002-6450-7551","position":11,"is_corresponding":false},{"id":991935,"name":"Luca Ferretti","orcid":"0000-0001-5044-8442","position":12,"is_corresponding":false},{"id":49023,"name":"Arkarachai Fungtammasan","orcid":"0000-0003-2398-0358","position":13,"is_corresponding":false},{"id":550054,"name":"Bettina Haase","orcid":"0000-0001-8945-7282","position":14,"is_corresponding":false},{"id":108064,"name":"Kerstin Howe","orcid":"0000-0003-2237-513X","position":15,"is_corresponding":false},{"id":550078,"name":"Woori Kwak","orcid":"0000-0003-0600-067X","position":16,"is_corresponding":false},{"id":991936,"name":"Gianluca Lombardo","orcid":"0000-0003-3641-5331","position":17,"is_corresponding":false},{"id":21312,"name":"Patrick Masterson","orcid":"0000-0001-8837-3706","position":18,"is_corresponding":false},{"id":991937,"name":"Graziella Messina","orcid":"0000-0001-8189-0727","position":19,"is_corresponding":false},{"id":991938,"name":"Anders Pape Møller","orcid":"0000-0003-3739-4675","position":20,"is_corresponding":false},{"id":30895,"name":"Jacquelyn Mountcastle","orcid":"0000-0003-1078-4905","position":21,"is_corresponding":false},{"id":747506,"name":"Timothy A. Mousseau","orcid":"0000-0002-2235-4868","position":22,"is_corresponding":false},{"id":226137,"name":"Joan Ferrer","orcid":"0000-0002-1184-5434","position":23,"is_corresponding":false},{"id":851754,"name":"Anna Olivieri","orcid":"0000-0002-3941-8098","position":24,"is_corresponding":false},{"id":21320,"name":"Arang Rhie","orcid":"0000-0002-9809-8127","position":25,"is_corresponding":false},{"id":772707,"name":"Diego Rubolini","orcid":"0000-0003-2703-5783","position":26,"is_corresponding":false},{"id":991939,"name":"Marielle Saclier","orcid":"0000-0002-5194-682X","position":27,"is_corresponding":false},{"id":793803,"name":"Roscoe Stanyon","orcid":"0000-0002-7229-1092","position":28,"is_corresponding":false},{"id":991940,"name":"David Stucki","orcid":"0000-0003-0131-9980","position":29,"is_corresponding":false},{"id":2130,"name":"Françoise Thibaud‐Nissen","orcid":"0000-0003-4957-7807","position":30,"is_corresponding":false},{"id":2115,"name":"James Torrance","orcid":"0000-0002-6117-8190","position":31,"is_corresponding":false},{"id":991941,"name":"Antonio Torroni","orcid":"0000-0002-4163-4478","position":32,"is_corresponding":false},{"id":346437,"name":"Kristina Weber","orcid":null,"position":33,"is_corresponding":false},{"id":628436,"name":"Roberto Ambrosini","orcid":"0000-0002-7148-1468","position":34,"is_corresponding":false},{"id":980575,"name":"Andrea Bonisoli‐Alquati","orcid":"0000-0002-9255-7556","position":35,"is_corresponding":false},{"id":21329,"name":"Erich  D. Jarvis","orcid":"0000-0001-8931-5049","position":36,"is_corresponding":false},{"id":991942,"name":"Luca Gianfranceschi","orcid":"0000-0002-7644-5968","position":37,"is_corresponding":false},{"id":21287,"name":"Giulio Formenti","orcid":"0000-0002-7554-5991","position":38,"is_corresponding":false},{"id":21322,"name":"Simona Secomandi","orcid":"0000-0001-8597-6034","position":0,"is_corresponding":true}],"reference_count":143,"raw_metadata":null,"created_at":"2026-07-19T01:08:11.275604Z","pmid":"36662619","pmcid":"PMC10044405","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":94.4444,"fair_a":50.0,"fair_i":80.0,"fair_r":50.0,"fair_zscore":1.77,"fair_rationale":{"fair_score":79.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":94.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Newly generated genomic resources (variants catalog, pangenome, Cactus alignment) This study Dataverse: https://doi.org/10.13130/RD_UNIMI/IDALZG","grounded":true,"rationale":"The paper provides a DOI for the genomic resources in the Dataverse repository.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Dataverse","grounded":true,"rationale":"The paper names the Dataverse repository as the holder for the genomic resources.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Newly generated genomic resources (variants catalog, pangenome, Cactus alignment) This study Dataverse: https://doi.org/10.13130/RD_UNIMI/IDALZG","grounded":true,"rationale":"The data availability statement points to the Dataverse repository with a DOI.","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Deposited data","grounded":true,"rationale":"The paper includes an itemised inventory (the Deposited data table) that lists the data types and identifiers. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Deposited data de novo assembly for Hirundo rustica This study RefSeq: GCF_015227805.1. Genbank: GCA_015227805.3, GCA_015227815.3. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are non-human, so no gatekeeper is needed.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state how long the data will be retained. [majority verdict 'no' (3/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":80.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"All vcf files were first filtered to remove variants falling within repetitive regions","grounded":true,"rationale":"The paper uses VCF, an open format, for variant files. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Functional gene completeness, measured with BUSCO, is 96%","grounded":false,"rationale":"The paper uses BUSCO, a community standard for assessing genome assembly completeness. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"Safran et al. 14 NCBI BioProject: PRJNA323498","grounded":true,"rationale":"The paper provides NCBI BioProject identifiers for publicly available datasets used.","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":50.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not specify a license for the data. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not specify a license for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Deposited data de novo assembly for Hirundo rustica This study RefSeq: GCF_015227805.1. 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[majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Functional gene completeness, measured with BUSCO, is 96%","why":"The paper uses BUSCO, a community standard for assessing genome assembly completeness. 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For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are non-human, so no gatekeeper is needed.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state how long the data will be retained. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:32:44.143555Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}