{"doi":"10.1093/jhered/esad047","title":"De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, <i>Aphelocoma californica</i>","abstract":"We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated \"Haplotype 1\") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.","journal":"Journal of Heredity","year":2023,"id":358666,"datarank":0.4273225439379834,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.054586546469783274,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.054586546469783274,"corpus_percentile":56.463216523555346,"corpus_rank":5629,"citation_count":11,"citer_count":7,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9343,"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":70.8333,"fair_percentile":91.99021705900336,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":92291,"name":"Merly Escalona","orcid":"0000-0003-0213-4777","position":1,"is_corresponding":false},{"id":1108315,"name":"Phred M. Benham","orcid":"0000-0003-3276-6177","position":2,"is_corresponding":false},{"id":730420,"name":"Mohan P A Marimuthu","orcid":"0000-0001-6121-3286","position":3,"is_corresponding":false},{"id":108056,"name":"Ruta Sahasrabudhe","orcid":"0000-0002-3285-6845","position":4,"is_corresponding":false},{"id":730421,"name":"Oanh Nguyen","orcid":"0000-0003-1492-2084","position":5,"is_corresponding":false},{"id":911241,"name":"Noravit Chumchim","orcid":"0000-0003-1139-9427","position":6,"is_corresponding":false},{"id":911242,"name":"Eric Beraut","orcid":"0000-0002-4443-6282","position":7,"is_corresponding":false},{"id":908281,"name":"Colin W Fairbairn","orcid":"0009-0007-8129-0095","position":8,"is_corresponding":false},{"id":24610,"name":"William Seligmann","orcid":"0000-0002-5762-3095","position":9,"is_corresponding":false},{"id":1108317,"name":"Rauri C. K. Bowie","orcid":"0000-0001-8328-6021","position":10,"is_corresponding":false},{"id":1108316,"name":"Carla Cicero","orcid":"0000-0002-6282-2339","position":11,"is_corresponding":false},{"id":19198,"name":"John E. McCormack","orcid":"0000-0002-0912-1461","position":12,"is_corresponding":false},{"id":98040,"name":"Robert K. Wayne","orcid":"0000-0003-3537-2245","position":13,"is_corresponding":false},{"id":19204,"name":"Devon A. DeRaad","orcid":"0000-0003-3105-985X","position":0,"is_corresponding":true}],"reference_count":58,"raw_metadata":null,"created_at":"2026-07-19T01:13:48.379546Z","pmid":"37589384","pmcid":"PMC10650945","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":81.25,"fair_i":20.0,"fair_r":58.3333,"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":"The assembled reference genomes presented here have been made immediately publicly available at: NCBI BioProject PRJNA904314 (Pseudo-haplotype 1; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA904314/ ) and NCBI BioProject PRJNA904313 (Pseudo-haplotype 2; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA904313/ )","grounded":true,"rationale":"The paper gives NCBI BioProject accessions (PRJNA904314, PRJNA904313), which are persistent identifier schemes.","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":"The assembled reference genomes presented here have been made immediately publicly available at: NCBI BioProject PRJNA904314","grounded":true,"rationale":"NCBI is named as the repository holding the data. 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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.","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":"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":"2026-07-20T12:23:24.832109Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}