A Super‐Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution

The main genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa whose radiation occurred in allopatry. In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies of C. medica, C. reticulata and C. micrantha, released for the first time alongside a published chromosome-scale assembly of C. maxima. Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA-satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the C. maxima assembly. Resequencing information from 55 accessions helped to explore the intra- and interspecific diversity of the ancestral taxa and their relationships with horticultural groups. Diagnostic SNPs of the ancestral taxa revealed interspecific introgressions in several representative accessions of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa. Diagnostic PAV analysis uncovered a large chloroplastic introgression in C. medica chromosome 4. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research.

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Publication Details

Journal
Plant Biotechnology Journal
Published
2026-02-03
DOI
https://doi.org/10.1111/pbi.70553
Primary Topic
Chromosomal and Genetic Variations
Type
article
Field-Weighted Citation Impact
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article

A Super‐Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution

Edson Mário de Andrade Silva, Gaëtan Droc, Fabienne Micheli, Alexandre Soriano et al.
Plant Biotechnology Journal
Chromosomal and Genetic Variations
article

A Super‐Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution

Edson Mário de Andrade Silva, Gaëtan Droc, Fabienne Micheli, Alexandre Soriano, Benjamin Istace, Franck Curk, Delphine Giraud, Bárbara Hufnagel, Arnaud Lemainque, Raner José Santana Silva, Fredson dos Santos Menezes, Florian Maumus, Pierre Mournet, François Luro, Simone Duprat, Caroline Belser, A. Dereeper, Corinne Cruaud, Maëva Miranda, Patrick Ollitrault, Patrick Wincker, Karine Labadie, Elodie Marchi, Gilles Costantino, Sylvain Santoni, Stéphanie Sidibe‐Bocs
article en

Abstract

The main genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa whose radiation occurred in allopatry. In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies of C. medica, C. reticulata and C. micrantha, released for the first time alongside a published chromosome-scale assembly of C. maxima. Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA-satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the C. maxima assembly. Resequencing information from 55 accessions helped to explore the intra- and interspecific diversity of the ancestral taxa and their relationships with horticultural groups. Diagnostic SNPs of the ancestral taxa revealed interspecific introgressions in several representative accessions of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa. Diagnostic PAV analysis uncovered a large chloroplastic introgression in C. medica chromosome 4. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research.

Plant Biotechnology Journal
Centre National de la Recherche Scientifique (FR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR), Agropolis International (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Universidade Estadual de Santa Cruz (BR), University of Florida (US), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Genoscope (FR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (FR), CEA Paris-Saclay (FR), Institut Agro Montpelier (FR), Institut de Recherche en Infectiologie de Montpellier (FR), Services déconcentrés d'appui à la recherche Occitanie-Montpellier (FR), Institut de Recherche pour le Développement (FR)
Institut Français de Bioinformatique, Agence Nationale de la Recherche, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de Montpellier
Life in Land
Openalex Percentile: Top 69%
Chromosomal and Genetic Variations
DOIOpen Access PDFOpenAlex
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