Integrative Morphometric, Sensory and Chloroplast DNA Evidence Clarifies Species Boundaries and Varietal Identities of Cucumis melo and Cucumis sativus Landraces in Sri Lanka

Sri Lanka harbors a culturally significant yet under-characterized diversity of Cucumis melo L. and Cucumis sativus L., much of which is absent from global germplasm repositories. To address longstanding taxonomic uncertainties and improve documentation of these genetic resources, we conducted an integrative assessment combining a nationwide germplasm survey, multivariate morphometric analyses, chloroplast DNA barcoding, phylogenetic reconstruction, and supporting sensory evaluation. Twenty representative genotypes collected from 632 sites were cultivated across three contrasting agro-ecological zones. Morphometric analyses consistently differentiated C. melo from C. sativus and resolved coherent intra-specific varietal groups that aligned with farmer-recognized classifications. Chloroplast phylogenies based on rbcL and trnH–psbA strongly supported species boundaries and conclusively placed both Thiyambara variants within C. sativus , while the feral Gon Kekiri accession grouped within divergent maternal lineages of C. melo . Divergence dating revealed deep Miocene-level diversification in C. melo compared with the relatively shallow chloroplast divergence observed in C. sativus , consistent with established Cucurbitaceae evolutionary chronograms. These findings provide the first robust taxonomic framework for Sri Lankan Cucumis , highlighting unique maternal lineages and farmer-maintained varietal identities of potential value for conservation, crop improvement, and future evolutionary research.