{ "abstract": "Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNPs fully discriminant of 20 Citrus species (diagnostic SNPs, DSNPs), enabling detailed exploration of inter- and intraspecific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.", "abstract_shown": true, "affiliations": [ "CIRAD, UMR AGAP Institute, Petit-Bourg F-97170, France.", "UMR AGAP Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34090 Montpellier, France.", "Fundo de Defesa da Citricultura, 14807-040, Araraquara, Brazil.", "UMR PHIM, IRD, F-34394 Montpellier, France.", "UMR AGAP, INRAE, Institut Agro Montpellier, CIRAD, University of Montpellier, F-20230 San Giuliano, France.", "Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry F-91057, France.", "Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry F-91057, France.", "UMR AGAP, INRAE, Institut Agro Montpellier, CIRAD, University of Montpellier, F-34060 Montpellier, France.", "Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil.", "CNRS/UPVD, Plant Genome and Development (LGDP), Perpignan F-66100, France.", "CIRAD, UMR AGAP Institut, F-34398 Montpellier, France.", "CIRAD, UMR AGAP Institut, F-20230 San Giuliano, France.", "Department of Agriculture and Fisheries, Bundaberg Research Station, Qld 4670 Bundaberg, Australia.", "Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain.", "Institut Agronomique Néo-Calédonien, Station de Recherche Agronomique de Pocquereux, 98880 La Foa, Nouvelle Calédonie.", "Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de 46022 Valencia, Valencia, Spain." ], "article_type": "research article", "arxiv": null, "author_total": 30, "authors": [ { "affs": [ 0, 1 ], "name": "Barbara Hufnagel", "orcid": "0000-0002-3515-2122" }, { "affs": [ 2 ], "name": "Monica Alves" }, { "affs": [ 0, 1 ], "name": "Quentin Piet" }, { "affs": [ 3 ], "name": "Alexis Dereeper", "orcid": "0000-0001-8120-8409" }, { "affs": [ 4 ], "name": "Delphine Giraud", "orcid": "0000-0002-1563-0123" }, { "affs": [ 2 ], "name": "Leny Calvez" }, { "affs": [ 5 ], "name": "Caroline Belser", "orcid": "0000-0002-8108-9910" }, { "affs": [ 6 ], "name": "Karine Labadie" }, { "affs": [ 5 ], "name": "Simone Duprat" }, { "affs": [ 6 ], "name": "Corinne Cruaud", "orcid": "0000-0002-4752-7278" }, { "affs": [ 5 ], "name": "Benjamin Istace" }, { "affs": [ 7 ], "name": "Franck Curk" }, { "affs": [ 8 ], "name": "Fredson Dos Santos Menezes" }, { "affs": [ 9 ], "name": "Khadidiatou Diop" }, { "affs": [ 1, 10 ], "name": "Maëva Miranda" }, { "affs": [ 1, 11 ], "name": "Yann Froelicher" }, { "affs": [ 12 ], "name": "Malcolm Smith" }, { "affs": [ 13 ], "name": "Pablo Aleza" }, { "affs": [ 14 ], "name": "Stéphane Lebegin" }, { "affs": [ 14 ], "name": "Carole Martin" }, { "affs": [ 1, 10 ], "name": "Fabienne Micheli" }, { "affs": [ 1, 10 ], "name": "Pierre Mournet" }, { "affs": [ 1, 10 ], "name": "Gaetan Droc", "orcid": "0000-0003-1849-1269" }, { "affs": [ 15 ], "name": "Leandro Peña" }, { "affs": [ 2 ], "name": "Nelson Wulff" }, { "affs": [ 1, 10 ], "name": "Raphaël Morillon" }, { "affs": [ 5 ], "name": "Patrick Wincker", "orcid": "0000-0001-7562-3454" }, { "affs": [ 5 ], "name": "Jean-Marc Aury" }, { "affs": [ 6 ], "name": "Arnaud Lemainque" }, { "affs": [ 1, 2, 10 ], "name": "Patrick Ollitrault" } ], "bibtex": "https://research.draconitic.com/paper/74844t0ct1msk.bib", "cited_by": 0, "doi": "10.1093/hr/uhag213", "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13719177/?tool=EBI", "id": "74844t0ct1msk", "issns": [ "2662-6810", "2052-7276" ], "landing_url": "https://europepmc.org/article/PMC/PMC13719177", "language": "eng", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1311|Genetic Mapping and Diversity in Plants and Animals" ] ], "openalex": "W4417341129", "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13719177/pdf/?tool=EBI", "pmcid": "PMC13719177", "pmid": "42960378", "published": "2026-06-02", "publisher": null, "ris": "https://research.draconitic.com/paper/74844t0ct1msk.ris", "sources": [ { "first_seen": "2026-10-31T00:20:39Z", "native_id": "PMC:PMC13719177", "source": "europepmc", "url": "https://europepmc.org/article/PMC/PMC13719177" }, { "first_seen": "2026-11-01T00:20:52Z", "native_id": "MED:42960378", "source": "europepmc", "url": "https://europepmc.org/article/MED/42960378" } ], "subjects": [ { "field": "biology", "origin": "openalex:1311|Genetic Mapping and Diversity in Plants and Animals", "subfield": "genetics-genomics" } ], "title": "Chromosome-scale genome assembly of Australian finger lime and resequencing reveal the hidden diversity of Oceanian citrus", "title_text": "Chromosome-scale genome assembly of Australian finger lime and resequencing reveal the hidden diversity of Oceanian citrus", "type": "peer-reviewed", "updated_at": "2026-11-02T03:21:46Z", "url": "https://research.draconitic.com/paper/74844t0ct1msk", "venue": "Horticulture research", "versions": [] }