Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Four Ottelia Species

The genus Ottelia comprises approximately 21 submerged macrophyte species primarily found in tropical Africa and Southeast Asia. The classification of several Ottelia species as vulnerable under the criteria “A2c” in the China Species Red List emphasizes the urgency of establishing a credible taxonomy. The ambiguity in taxonomy and evolutionary history persists, primarily stemming from the absence of a robust phylogeny at the species level. The rapid progress in high-throughput sequencing technology has facilitated the retrieval of complete chloroplast (cp) genome sequences, offering a molecular foundation for conducting phylogenetic analyses. In this study, the entire cp genomes of five samples of four Ottelia species were sequenced. All five Ottelia samples exhibited a circular, quadripartite-structured molecule, with lengths ranging from 156,823 to 162,442 bp. A total of 75–88 simple sequence repeats (SSRs) in the cp genomes of the five Ottelia samples were observed, which could be used for species identification. A preliminary phylogenetic analysis revealed that O. fengshanensis, O. acuminata, and O. guanyangensis clustered with strong support (100 BS). O. acuminata var. jingxiensis was resolved as a sister to O. acuminata var. lunanensis (100 BS), and both were further found to be sisters to O. balansae. The widely distributed O. alismoides exhibited a close phylogenetic relationship as the sister taxon to all the Chinese endemic taxa, supported by robust values. Together, our thorough examination of the entire cp genomes of the five Ottelia samples provides eminent insights into reconstructing their phylogeny. Furthermore, it illuminates the evolutionary dynamics of the cp genome within the Ottelia genus.