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.

Citrullus amarus (citronmelon) 是一种重要的作物，对多种病害具有抗性。叶绿体基因组在研究植物的遗传进化中很重要。所述C.苦竹叶绿体基因组在本研究中使用基于全基因组测序的新的装配方法首次报道。我们用 313 种西瓜材料在叶绿体基因组中鉴定了 82 个 SNP 位点。82 个 SNP 可以有效地将天然西瓜种群分为四组：C. lanatus subsp 。lanatus , C. lanatus subsp . mucosospermus , C. lanatus subsp . vulgaris（生态学上来自美洲）和C. lanatus subsp. vulgaris（来自亚洲的生态学），遗传多样性（π）递减（分别为 6.6 × 10 ^-5、2.4 × 10 ^-5、9.8 × 10 ^-6和 5.41 × 10 ^-6）。C. lanatus subsp 的单果重、可溶性固形物、果实颜色和千粒重。lanatus与其他三组显着不同。这些结果表明，完整的叶绿体基因组可用于西瓜群体遗传学的研究，有助于种​​内亚群的分类和核心种质资源的鉴定。