{"doi":"10.1093/molbev/msae036","title":"A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography","abstract":"The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.","journal":"Molecular Biology and Evolution","year":2024,"id":424069,"datarank":0.6435118364411256,"base_score":3.1354942159291497,"endowment":3.1354942159291497,"self_citation_contribution":0.47032413238937254,"citation_network_contribution":0.17318770405175316,"self_endowment_contribution":0.47032413238937254,"citer_contribution":0.17318770405175316,"corpus_percentile":69.18078440473428,"corpus_rank":3985,"citation_count":22,"citer_count":17,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8972,"is_data_producer":true,"deposit_databanks":{"GENBANK":["GCA_009873245.3","GCA_008658375.2.","CM018075.1"],"SRA":["SRX6360705"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":70.8333,"fair_percentile":91.99021705900336,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":844618,"name":"Phillip A. Morin","orcid":"0000-0002-3279-1519","position":1,"is_corresponding":false},{"id":112137,"name":"Susanne Meyer","orcid":null,"position":2,"is_corresponding":false},{"id":514521,"name":"Li‐Fang Chu","orcid":"0000-0002-4738-4481","position":3,"is_corresponding":false},{"id":959269,"name":"Jeff K. Jacobsen","orcid":"0000-0002-5972-3292","position":4,"is_corresponding":false},{"id":3802,"name":"Jessica Antosiewicz‐Bourget","orcid":"0000-0002-9676-1642","position":5,"is_corresponding":false},{"id":491719,"name":"Daniel Mamott","orcid":"0000-0001-9959-546X","position":6,"is_corresponding":false},{"id":987043,"name":"Maylie Gonzales","orcid":null,"position":7,"is_corresponding":false},{"id":565119,"name":"Cara Argus","orcid":"0000-0002-7584-5062","position":8,"is_corresponding":false},{"id":514524,"name":"Jennifer M. Bolin","orcid":"0000-0002-2502-6982","position":9,"is_corresponding":false},{"id":350044,"name":"Mark E. Berres","orcid":"0000-0001-6282-0117","position":10,"is_corresponding":false},{"id":30838,"name":"Olivier Fédrigo","orcid":"0000-0002-6450-7551","position":11,"is_corresponding":false},{"id":513710,"name":"John Steill","orcid":"0000-0003-2994-3400","position":12,"is_corresponding":false},{"id":109574,"name":"Scott Swanson","orcid":"0000-0002-3314-0515","position":13,"is_corresponding":false},{"id":443984,"name":"Peng Jiang","orcid":"0000-0002-6057-7624","position":14,"is_corresponding":false},{"id":21320,"name":"Arang Rhie","orcid":"0000-0002-9809-8127","position":15,"is_corresponding":false},{"id":21287,"name":"Giulio Formenti","orcid":"0000-0002-7554-5991","position":16,"is_corresponding":false},{"id":2122,"name":"Adam  M. Phillippy","orcid":"0000-0003-2983-8934","position":17,"is_corresponding":false},{"id":19563,"name":"Robert S. Harris","orcid":"0000-0001-5464-6892","position":18,"is_corresponding":false},{"id":2132,"name":"Jonathan M. D. Wood","orcid":"0000-0002-7545-2162","position":19,"is_corresponding":false},{"id":108064,"name":"Kerstin Howe","orcid":"0000-0003-2237-513X","position":20,"is_corresponding":false},{"id":850636,"name":"Bogdan Kirilenko","orcid":"0000-0002-9394-4275","position":21,"is_corresponding":false},{"id":894808,"name":"Chetan Munegowda","orcid":"0000-0002-3790-2185","position":22,"is_corresponding":false},{"id":51339,"name":"Michael Hiller","orcid":"0000-0003-3024-1449","position":23,"is_corresponding":false},{"id":558775,"name":"Aashish Jain","orcid":"0000-0001-7580-8694","position":24,"is_corresponding":false},{"id":316939,"name":"Daisuke Kihara","orcid":"0000-0003-4091-6614","position":25,"is_corresponding":false},{"id":262200,"name":"J. Spencer Johnston","orcid":"0000-0003-4792-2945","position":26,"is_corresponding":false},{"id":987044,"name":"Alexander Ionkov","orcid":null,"position":27,"is_corresponding":false},{"id":425611,"name":"Kalpana Raja","orcid":"0000-0002-3156-4197","position":28,"is_corresponding":false},{"id":894806,"name":"Huishi Toh","orcid":"0000-0002-8843-8263","position":29,"is_corresponding":false},{"id":729800,"name":"Aimée R. Lang","orcid":"0000-0001-9620-8436","position":30,"is_corresponding":false},{"id":986591,"name":"Magnus Wolf","orcid":"0000-0001-9212-9861","position":31,"is_corresponding":false},{"id":21329,"name":"Erich  D. Jarvis","orcid":"0000-0001-8931-5049","position":32,"is_corresponding":false},{"id":443986,"name":"James A. Thomson","orcid":"0000-0003-2970-942X","position":33,"is_corresponding":false},{"id":19738,"name":"Mark J. P. Chaisson","orcid":"0000-0001-5395-1457","position":34,"is_corresponding":false},{"id":3794,"name":"Ron Stewart","orcid":"0000-0002-9041-1828","position":35,"is_corresponding":false},{"id":894809,"name":"Yury V. Bukhman","orcid":"0000-0002-8111-7651","position":0,"is_corresponding":true}],"reference_count":148,"raw_metadata":null,"created_at":"2026-07-19T01:58:07.191194Z","pmid":"38376487","pmcid":"PMC10919930","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":62.5,"fair_i":20.0,"fair_r":50.0,"fair_zscore":1.4401,"fair_rationale":{"fair_score":70.83,"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":"Primary pseudohaplotype assembly is mBalMus1.pri.v3, RefSeq accession GCF_009873245.2, and GenBank accession GCA_009873245.3 .","grounded":true,"rationale":"The paper provides a RefSeq accession (GCF_009873245.2), which is a persistent identifier in the PID scheme.","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":"Primary pseudohaplotype genome assembly and annotation are available from NCBI Genome, id 7017 ( National Center for Biotechnology Information (US) 2022b ).","grounded":true,"rationale":"NCBI is a named data repository.","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":"Raw sequencing and mapping data and various versions of genome assemblies are available from VGP GenomeArk ( Vertebrate Genomes Project 2022a : 1; Vertebrate Genomes Project 2022b ). Primary pseudohaplotype genome assembly and annotation are available from NCBI Genome, id 7017 ( National Center for Biotechnology Information (US) 2022b ). Primary pseudohaplotype assembly is mBalMus1.pri.v3, RefSeq accession GCF_009873245.2, and GenBank accession GCA_009873245.3 . Alternate pseudohaplotype assembly is mBalMus1.alt.v2, GenBank accession GCA_008658375.2 . Mitochondrion assembly generated in this study has GenBank accession CM018075.1 . Fibroblast transcriptomics data have been deposited to the NCBI SRA archive. Iso-seq accession SRX6360705, Illumina RNA-seq accession SRX7696402. 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Primary pseudohaplotype genome assembly and annotation are available from NCBI Genome, id 7017 ( National Center for Biotechnology Information (US) 2022b ). Primary pseudohaplotype assembly is mBalMus1.pri.v3, RefSeq accession GCF_009873245.2, and GenBank accession GCA_009873245.3 . Alternate pseudohaplotype assembly is mBalMus1.alt.v2, GenBank accession GCA_008658375.2 . Mitochondrion assembly generated in this study has GenBank accession CM018075.1 . Fibroblast transcriptomics data have been deposited to the NCBI SRA archive. Iso-seq accession SRX6360705, Illumina RNA-seq accession SRX7696402. Additional supplementary materials and datasets are available on OSF ( Bukhman et al. 2019 ).","grounded":true,"rationale":"The Data Availability section provides an itemised inventory of the dataset components, including specific assemblies and accessions. [majority verdict 'yes' (4/5 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":"Primary pseudohaplotype assembly is mBalMus1.pri.v3, RefSeq accession GCF_009873245.2, and GenBank accession GCA_009873245.3 .","grounded":true,"rationale":"The dataset identifier appears only in the body text, not as a reference-list entry. 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[majority verdict 'yes' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No reuse license is stated for the data; the article's CC-BY license does not apply to the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format for the released data is named in the text.","gain":8.33,"priority":"important","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":"Primary pseudohaplotype assembly is mBalMus1.pri.v3, RefSeq accession GCF_009873245.2, and GenBank accession GCA_009873245.3 .","why":"The dataset identifier appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"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.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Raw sequencing and mapping data and various versions of genome assemblies are available from VGP GenomeArk ( Vertebrate Genomes Project 2022a : 1; Vertebrate Genomes Project 2022b ).","why":"The paper describes how to access the data via repositories, but does not apply an explicit access-level label like 'open access'. [majority verdict 'partial' (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":"no","current":0.0,"evidence":null,"why":"No community-standard data/metadata vocabulary (e.g., MIAME, GO) is named for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No README, data dictionary, or codebook is mentioned as accompanying the data.","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. 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 not human or sensitive; no gatekeeper is mentioned.","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":"No sentence in the paper states when the data become available or how long they persist. [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.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","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."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:49:00.519726Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}