Complete chloroplast genomes of three cultivated Cucurbita species: insights into adaptive evolution, phylogenetic relationship, and cpSSR marker development

Abstract Background: Cucurbita moschata, C. maxima, and C. argyrosperma are the most well-known horticultural crops of the Cucurbitafamily. These Cucurbita species are taxonomically and phylogenetically puzzling resulted from similar feature and interspecies hybridization. Results: The complete chloroplast genome size of C. moschata, C. maxima, and C. argyrosperma were assembled and studied for the first time in this study, with genome sizes of 157,644, 157,204, and 157,809bp, respectively. The 130 annotated genes were identified in these genomes, comprising eight rRNA, 37 tRNA, and 85 protein-coding genes, were organized into conserved quadripartite circular topologies. A comparison within Cucurbitashowed that the highly variable region (trnL-ndhJ) was identified to serve a specific DNA barcode, and three genes (atpE, clpP, and ycf1) showed significant selective sites under positive selection. Phylogenetic analysis confirmed that the five cultivated crops of Cucurbita were clustered into one monophyletic group, suggesting that the completion of more chloroplast genomes would help clarify the phylogenetic relationship among Cucurbita. Additionally, ten polymorphic SSRs were identified, which can be used to explore the evolutionary relationships and identify Cucurbita. Conclusion: These results will help identify the species, molecular breeding, adaptive evolution, and phylogenetic relationshipsof Cucurbita.