Comparative and phylogenetic analyses of plastid genomes of the medicinally important genus Alisma (Alismataceae)

<i>Alisma</i> L. is a medicinally important genus of aquatic and wetland plants consisting of c. 10 recognized species. However, largely due to polyploidy and limited taxon and gene sampling, the phylogenomic relationships of <i>Alisma</i> remain challenging. In this study, we sequenced 34 accessions of Alismataceae, including eight of the ten species of <i>Alisma</i>, one species of <i>Echinodorus</i> and one species of <i>Luronium</i>, to perform comparative analyses of plastid genomes and phylogenetic analyses. Comparative analysis of plastid genomes revealed high sequence similarity among species within the genus. Our study analyzed structural changes and variations in the plastomes of <i>Alisma</i>, including IR expansion or contraction, and gene duplication or loss. Phylogenetic results suggest that <i>Alisma</i> is monophyletic, and constitutes four groups: (1) <i>A. lanceolatum</i> and <i>A. canaliculatum</i>; (2) the North American clade of <i>A. subcordatum</i> and <i>A. triviale</i>; (3) <i>A. wahlenbergii</i> and <i>A. gramineum</i>; and (4) <i>A. plantago-aquatica</i> from Eurasia and northern Africa with the eastern Asian <i>A. orientale</i> nested within it. Hence the results challenge the recognition of <i>A. orientale</i> as a distinct species and raise the possibility of treating it as a synonym of the widespread <i>A. plantago-aquatica</i>. The well-known <i>Alismatis Rhizoma</i> (Zexie) in Chinese medicine was likely derived from the morphologically variable <i>Alisma plantago-aquatica</i> throughout its long history of cultivation in Asia. The plastome phylogenetic results also support the tetraploid <i>A. lanceolatum</i> as the likely maternal parent of the hexaploid eastern Asian <i>A. canaliculatum</i>.