Comparative Plastid Genome and Phylogenomic Analyses of Species.

Potamogetonaceae are aquatic plants divided into six genera. The largest genus in the family is , which is morphologically diverse with many hybrids and polyploids. Potamogetonaceae plastomes were conserved in genome size (155,863 bp-156,669 bp), gene contents (113 genes in total, comprising 79 protein-coding genes and 30 tRNA and 4 rRNA genes), and GC content (36.5%). However, we detected a duplication of the gene in the IR region of the and plastomes. A comparative analysis of Alismatales indicated that the plastomes of Potamogetonaceae, Cymodaceae, and Ruppiaceae have experienced a 6-kb inversion of the region and the complex has been lost in the plastome. Five divergent hotspots (, intron, , , and ) were identified among the plastomes, which will be useful for species identification. Phylogenetic analyses showed that the family Potamogetonaceae is a well-defined with 100% bootstrap support and divided into two different clades, and . Compared to the nucleotide substitution rates among Alismatales, we found neutral selection in all plastid genes of species. Our results reveal the complete plastome sequences of species, and will be helpful for taxonomic identification, the elucidation of phylogenetic relationships, and the plastome structural analysis of aquatic plants.