Chromosome-scale genome assembly of Australian finger lime and resequencing reveal the hidden diversity of Oceanian citrus

@article{hufnagel2026chromosomescale,
  title = {{Chromosome-scale genome assembly of Australian finger lime and resequencing reveal the hidden diversity of Oceanian citrus}},
  author = {Barbara Hufnagel and Monica Alves and Quentin Piet and Alexis Dereeper and Delphine Giraud and Leny Calvez and Caroline Belser and Karine Labadie and Simone Duprat and Corinne Cruaud and Benjamin Istace and Franck Curk and Fredson Dos Santos Menezes and Khadidiatou Diop and Maëva Miranda and Yann Froelicher and Malcolm Smith and Pablo Aleza and Stéphane Lebegin and Carole Martin and Fabienne Micheli and Pierre Mournet and Gaetan Droc and Leandro Peña and Nelson Wulff and Raphaël Morillon and Patrick Wincker and Jean-Marc Aury and Arnaud Lemainque and Patrick Ollitrault},
  journal = {Horticulture research},
  year = {2026},
  month = jun,
  doi = {10.1093/hr/uhag213},
  url = {https://europepmc.org/article/PMC/PMC13719177},
  note = {CC BY},
}

TY  - JOUR
TI  - Chromosome-scale genome assembly of Australian finger lime and resequencing reveal the hidden diversity of Oceanian citrus
AU  - Barbara Hufnagel
AU  - Monica Alves
AU  - Quentin Piet
AU  - Alexis Dereeper
AU  - Delphine Giraud
AU  - Leny Calvez
AU  - Caroline Belser
AU  - Karine Labadie
AU  - Simone Duprat
AU  - Corinne Cruaud
AU  - Benjamin Istace
AU  - Franck Curk
AU  - Fredson Dos Santos Menezes
AU  - Khadidiatou Diop
AU  - Maëva Miranda
AU  - Yann Froelicher
AU  - Malcolm Smith
AU  - Pablo Aleza
AU  - Stéphane Lebegin
AU  - Carole Martin
AU  - Fabienne Micheli
AU  - Pierre Mournet
AU  - Gaetan Droc
AU  - Leandro Peña
AU  - Nelson Wulff
AU  - Raphaël Morillon
AU  - Patrick Wincker
AU  - Jean-Marc Aury
AU  - Arnaud Lemainque
AU  - Patrick Ollitrault
PY  - 2026
DA  - 2026/06/02
JO  - Horticulture research
DO  - 10.1093/hr/uhag213
UR  - https://europepmc.org/article/PMC/PMC13719177
AB  - 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.
SN  - 2662-6810
SN  - 2052-7276
ER  -