Comparative Genomics and Phylogenetic Analyses of Aquarius macrophyllus and Related Genera in Alismataceae Based on Plastome Data

Abstract

ABSTRACT Aquarius macrophyllus, an aquatic species native to South America, has been widely utilized as an ornamental plant. Although the plastome data have been commonly used in plant evolution and phylogenetics, research on the plastome of A. macrophyllus remains scarce. In this study, we sequenced the plastome of A. macrophyllus and conducted a comparative analysis incorporating eight species from related genera of Caldesia, Sagittaria, Alisma, and Luronium. The assembled plastome was 180,860 bp in size, with 133 genes annotated, including 88 protein‐coding genes, 8 rRNA, and 37 tRNA. Comparative analyses showed that the genome lengths of the nine plastomes ranged from 159,063 to 180,860 bp, including a large single copy (LSC, 89,203–99,125 bp), a small single copy (SSC, 10,131–19,753 bp), and a pair of inverted repeat sequences (IR, 25,124–39,664 bp). The nine plastomes were similar in GC content, codon usage, and gene distribution but contained variations, including IR expansion in A. macrophyllus, loss of trnV‐UAC introns, and gene inversion in Caldesia and Sagittaria species. Two sequence inversions of 5.6 and 6.4 kb were detected in Sagittaria and Caldesia, respectively. A total of 532 simple sequence repeats (SSRs) and 667 dispersed repeats were detected in the nine plastomes. Selection pressure analysis using A. macrophyllus as a reference to compare with other species revealed that three ribosomal protein genes rps2, rps18, and rps7 were positively selected, which showed intergeneric specificity, especially displaying higher selection pressure in Sagittaria species than that in Caldesia species. Phylogenetic analysis of Alismataceae elucidated that Alisma, Luronium, and Burnatia species were early diverged, followed by Hydrocleys and Limnocharis. The monophyly of Aquarius and its sister relationship with Echinodorus were revealed, supporting the classification of the new genus Aquarius. Our study enriches the genomic resources of Aquarius and provides new insights into plastome structure and evolution in Alismataceae.

Keywords

• Alismataceae
• Aquarius macrophyllus
• comparative genomics
• phylogenetics
• plastome