Abstract
Citrullus amarus (citronmelon) is an important crop with resistance to many diseases. The chloroplast genome is important in studying the genetic evolution of plants. The C. amarus chloroplast genome was first reported in this study using a novel assembly method based on whole genome sequencing. We identified 82 SNP sites in chloroplast genome with 313 watermelon materials. The 82 SNPs could effectively divide the natural watermelon population into four groups: C. lanatus subsp. lanatus, C. lanatus subsp. mucosospermus, C. lanatus subsp. vulgaris (ecologically from the Americas) and C. lanatus subsp. vulgaris (ecologically from Asia), with decreasing genetic diversity (π) (6.6 × 10(-5), 2.4 × 10(-5), 9.8 × 10(-6) and 5.41 × 10(-6), respectively). The single fruit weight, soluble solids, fruit color and 1000-seed weight of C. lanatus subsp. lanatus were significantly different from those of the other three groups. These results indicate that the complete chloroplast genome can be used in studying population genetics of watermelon, which is helpful for classification among intra species subgroups and identification of core germplasm resources.