Integrative morphological, palynological, and phylogenomic evidence supports the recognition of Hongdaicitrus as a new genus within Citrus sensu lato.

Resolving the evolutionary relationships and generic boundaries of Citrus sensu lato (s.l.) remains a major challenge in plant systematics, largely because complex reticulate evolution and insufficient sampling of wild lineages have obscured the recognition of independent evolutionary entities. Here, we describe Hongdaicitrus gen. nov. and Hongdaicitrus xiangtoushanensis sp. nov., a new genus and species within Citrus s.l., from Guangdong Province, southern China. The new genus is characterized by imbricate petals that remain semi-closed, campanulate to tubular, and incompletely expanded at anthesis; 19-20 stamens arranged in three whorls, with distinctly unequal filaments connate into five fascicles; a 5-loculed ovary, short terete style, and conical stigma; and absent or highly reduced juice vesicles. Pollen micromorphological observations further support its distinctiveness, showing four relatively shallow germination sulci and densely perforate to finely foveolate exine ornamentation with small and relatively uniform lumina. Phylogenomic analyses based on 83 plastid protein-coding sequences and 5, 873 single-copy nuclear genes consistently recovered Hongdaicitrus as a deeply divergent lineage sister to Fortunella and clearly separated from Citrus s.s. Genome-wide resequencing analyses further showed that Hongdaicitrus forms a distinct genetic cluster and is clearly differentiated from Fortunella, Citrus s.s., Papeda, Poncirus, and other citrus relatives. Ecologically, Hongdaicitrus is endemic to rock crevices of exposed granite outcrops with extremely barren soils. Based on the IUCN Red List criteria, Hongdaicitrus xiangtoushanensis is provisionally assessed as Critically Endangered (CR). Our integrative evidence supports the recognition of Hongdaicitrus as a distinct genus, provides new insights into generic delimitation, systematics, and biogeographic diversification among Citrus s.l.