The first complete chloroplast genomes of two Alismataceae species, and the phylogenetic relationship under order Alismatales

Alismatales play an important role in the systematics of angiosperm, yet different phylogenetic topologies of Alismatales based on different species have been generated from several studies. Here we reported and characterized the first complete chloroplast (cp) genomes of two Alismataceae species, Alisma plantago-aquatica and Sagittaria trifolia, and analyzed the phylogenomic relationship of Alismatales based on the complete chloroplast sequences of 21 Alismatales species. The two chloroplast genomes have the typical quadripartite structure with 113 genes in total, including 79 protein-encoding genes, 30 transfer RNA genes and four ribosomal RNA genes. Both IR regeions of plastid genomes contain 8 protein-encoding genes, 7 tRNA genes and all the four rRNA genes. The genome of A. plantago-aquatica is 177,417 bp in length, with an overall G + C content of 35.7%, and the genome of Sagittaria trifolia is 167,642 bp in length, with an overall G + C content of 37.0%. Phylogenetic study showed that the three Alismataceae species comprise a monophyletic group with a high support rate, which was a sister to the Hydrocharitaceae clade. The core Alismatids, consisting of Potamogetonaceae, Zosteraceae, Hydrocharitaceae and Alismataceae, is sister to Tofieldiaceae. Alocasia macrorrhizos of Araceae is the basal taxon of Alismatales, and the other twelve Araceae species formed a sister group to the clade Tofieldaceae and core Alismatids.