Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure

Citrullus ecirrhosus , Citrullus rehmii , and Citrullus naudinianus are three important related wild species of watermelon in the genus Citrullus , and their morphological differences are clear, however, their chloroplast genome differences remain unknown. This study is the first to assemble, analyze, and publish the complete chloroplast genomes of C. ecirrhosus , C. rehmii , and C. naudinianus . A comparative analysis was then conducted among the complete chloroplast genomes of seven extant Citrullus species, and the results demonstrated that the average genome sizes of Citrullus is 157,005 bp, a total of 130–133 annotated genes were identified, including 8 rRNA, 37 tRNA and 85–88 protein-encoding genes. Their gene content, order, and genome structure were similar. However, noncoding regions were more divergent than coding regions, and rps16-trnQ was a hypervariable fragment. Thirty-four polymorphic SSRs, 1,271 SNPs and 234 INDELs were identified. Phylogenetic trees revealed a clear phylogenetic relationship of Citrullus species, and the developed molecular markers (SNPs and rps16-trnQ ) could be used for taxonomy in Citrullus . Three genes ( atpB , clpP1 , and rpoC2 ) were identified to undergo selection and would promote the environmental adaptation of Citrullus .