Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae)

Abstract

Background Hydrocharis L. and Limnobium Rich. are small aquatic genera, including three and two species, respectively. The taxonomic status, phylogenetic relationships and biogeographical history of these genera have remained unclear, owing to the lack of Central African endemic H. chevalieri from all previous studies. We sequenced and assembled plastomes of all three Hydrocharis species and Limnobium laevigatum to explore the phylogenetic and biogeographical history of these aquatic plants. Results All four newly generated plastomes were conserved in genome structure, gene content, and gene order. However, they differed in size, the number of repeat sequences, and inverted repeat borders. Our phylogenomic analyses recovered non-monophyletic Hydrocharis. The African species H. chevalieri was fully supported as sister to the rest of the species, and L. laevigatum was nested in Hydrocharis as a sister to H. dubia. Hydrocharis-Limnobium initially diverged from the remaining genera at ca. 53.3 Ma, then began to diversify at ca. 30.9 Ma. The biogeographic analysis suggested that Hydrocharis probably originated in Europe and Central Africa. Conclusion Based on the phylogenetic results, morphological similarity and small size of the genera, the most reasonable taxonomic solution to the non-monophyly of Hydrocharis is to treat Limnobium as its synonym. The African endemic H. chevalieri is fully supported as a sister to the remaining species. Hydrocharis mainly diversified in the Miocene, during which rapid climate change may have contributed to the speciation and extinctions. The American species of former Limnobium probably dispersed to America through the Bering Land Bridge during the Miocene.

Hydrocharis laevigata in Europe

“…Phylogenomic, morphological, and anatomical evidence strongly suggest a new vision of the genus Hydrocharis L. [ 16 , 17 ], one that includes the species of Limnobium Rich., usually considered to be a separate genus by World Flora Online (WFO) [ 18 ]. Assuming the species’ reclassification, there are currently five known members of the genus Hydrocharis L. Three are spread throughout Afro-Asia, and the other two are found from Mexico to northern Argentina and in the Caribbean.…”

“…With regards to sexual reproduction, the species mainly utilises wind pollination [ 17 , 22 , 28 ]. However, water pollination has also been observed, as has insect pollination, mediated by tiny aphid nymphs (Aphididae) and the aphids’ predators, ladybird beetles (Coccinellidae) [ 24 ].…”

The dynamic history of plastome structure across aquatic subclass Alismatidae

“…Total genomic DNA extraction, DNA fragmentation and preparation of sequencing libraries of all 13 newly sampled species followed the description by Li et al [ 31 ]. Genome skimming per sample was conducted on the Illumina HiSeq 2000 platform in Novogene (Tianjin, China), with 150 bp paired-end reads.…”

“…eight families and 20 genera, have been assembled and are available from GenBank (accessed on 1 January 2022). However, some genera have been extensively sampled (e.g., Ottelia [ 30 ]; Hydrocharis [ 31 ]), certain families lack accessible plastome resources. Thus, a comprehensive comparison of plastomes across Alismatidae remains scarce in the existing investigations.…”

Climate Change Potentially Leads to Habitat Expansion and Increases the Invasion Risk of Hydrocharis (Hydrocharitaceae)

“…ex Willd.) Byng & Christenh., H. morsus-ranae L., and H. spongia Bosc, has native ranges which span different continents without overlapping [ 15 ]. In the past, H. laevigata and H. spongia were treated as species in Limnobium Rich.…”