ArticlePlant biotechnology journal2026
A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.
Article in Plant biotechnology journal, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Investigation of allele-specific expression in citrus hybrids reveals the association between siRNA-mediatedHorticulture research · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Haplotype-resolved genome of Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil.Scientific data · 2026Article
- Citrus genomes: past, present and future.Horticulture research · 2025Article
- Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes.BMC genomic data · 2025Article
- Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.BMC plant biology · 2025Article
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Authors and funding
28 authors.
Funding
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.
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