Chromosome-level genomes of three invasive Cucurbitaceae species provide insights into genomic features associated with invasiveness

Several Cucurbitaceae species are invasive weeds threatening agriculture and ecosystems worldwide, yet their genomic resources remain limited, hampering efforts to elucidate the molecular basis of their rapid expansion and competitive success. Using an integrated sequencing strategy combining PacBio HiFi, Illumina short-read, and Hi-C technologies, we generated chromosome-scale genome assemblies for three invasive cucurbit species: Sicyos angulatus (597.41 Mb), Echinocystis lobata (629.27 Mb), and Melothria pendula (276.42 Mb). The resulting assemblies demonstrate high contiguity, with scaffold N50 values reaching 50.69 Mb, 32.59 Mb, and 22.38 Mb respectively, and exceptional completeness, achieving BUSCO scores exceeding 98% for all three genomes. Comparative analysis encompassing 26 Cucurbitaceae species revealed that lineage-specific dynamics of long terminal repeat retrotransposons are the primary correlate of genome size variation, with most insertion events occurring within the past two million years. A lineage-specific whole-genome duplication event confined to tribe Sicyoeae was detected, supported by markedly younger Ks peaks in S. angulatus and E. lobata . Analysis of gene family evolution identified lineage-specific expansions in pathways linked to invasiveness: signal transduction and stress response genes in S. angulatus , carbohydrate metabolism and protein synthesis components in E. lobata , and secondary metabolite biosynthesis pathways in M. pendula . The identified genomic features, including recent retrotransposon proliferation, lineage-specific polyploidization, and expansion of stress-responsive gene families, may collectively contribute to traits plausibly linked to the competitive success of these species, though functional validation is required.