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In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super\u2010pangenome for cultivated citrus, established with de novo assemblies of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009medica<\/jats:italic>\n                    <\/jats:styled-content>\n                    ,\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009reticulata<\/jats:italic>\n                    <\/jats:styled-content>\n                    and\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009micrantha<\/jats:italic>\n                    <\/jats:styled-content>\n                    , released for the first time alongside a published chromosome\u2010scale assembly of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009maxima<\/jats:italic>\n                    <\/jats:styled-content>\n                    . Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA\u2010satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009maxima<\/jats:italic>\n                    <\/jats:styled-content>\n                    assembly. Resequencing information from 55 accessions helped to explore the intra\u2010 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\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009reticulata<\/jats:italic>\n                    <\/jats:styled-content>\n                    ,\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009maxima<\/jats:italic>\n                    <\/jats:styled-content>\n                    and\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009medica<\/jats:italic>\n                    <\/jats:styled-content>\n                    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\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C.\u2009medica<\/jats:italic>\n                    <\/jats:styled-content>\n                    chromosome 4. The analysis of the functional enrichment and species\u2010specific adaptations in the citrus super\u2010pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super\u2010pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research.\n                  <\/jats:p>","DOI":"10.1111\/pbi.70553","type":"journal-article","created":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T09:28:57Z","timestamp":1770110937000},"page":"3345-3367","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A Super\u2010Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution"],"prefix":"10.1111","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1849-1269","authenticated-orcid":false,"given":"Gaetan","family":"Droc","sequence":"first","affiliation":[{"name":"UMR AGAP, Institut Agro Montpellier, CIRAD, INRAE University of Montpellier  Montpellier France"},{"name":"UMR AGAP, CIRAD  Montpellier 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