Resolution of Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

Abstract

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists probably due to its position as a basal-angiosperm. The phylogenetic relationships within the order have well been studied and resolved; however, a few controversial nodes still remain in the Nymphaeaceae including the position of the genus Nuphar. The position of the genus Nuphar and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of completely sequenced plastid genomes of the Nymphaeales and applies large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first one for the monotypic genus Euryale. Using a set of 66 protein coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with a convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident particularly in the contraction/expansion of the Inverted Repeat regions and in RNA editing events. Genome structure, gene content and arrangement were highly conserved among the chloroplast genomes.

Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae

“…In the last decade, several systematic studies of the water lily family were conducted by combining morphological and molecular evidence. Based on molecular and morphological evidence, multiple studies support Brachyceras, Anecphya, Nymphaea, Hydrocallis, Lotos as a monophyletic subgenera, respectively, in agreement with our results (Borsch et al, 2007;LÖHNE et al, 2007;Borsch et al, 2008;Taylor, 2008;He et al, 2018). The combined morphological and molecular analyses conducted by Borsch et al (2008) suggest that the genus Nymphaea is paraphyletic, with the subgenus Nymphaea being sister to a clade comprising the other subgenus and the Euryale-Victoria clade.…”

“…However, the monophyly of Nymphaeaceae and the status of the other two families remain controversial (Biswal et al, 2012;Gruenstaeudl et al, 2017). Our results corroborate that Nymphaeaceae is monophyletic, represented by four genera, confirmed by plastid genomes, and Cabombaceae containing two genera of Cabomba and Brasenia is determined to be a sister to Nymphaeaceae (He et al, 2018). We further reconstructed a robust Nymphaeales phylogeny which is consistent with the previous study (Zhang et al, 2020).…”

“…As shown in Figure 2, four step-wise filtered data sets of low copy-number orthogroups (OGs) (1,141 OGs, 942 OGs, 882 OGs, 686 OGs) were used to reconstruct phylogenetic relationships using the coalescent method based on species coverage and length of aligned matrixes (see Methods and Figures 2, 3). Among the four sampled Nymphaeaceae genera, Nuphar was determined to be the earliest diverging lineage, in agreement with previous phylogenetic results of chloroplastid genomes with 66 plastid protein codon genes from 13 Nymphaeaceae species (Gruenstaeudl et al, 2017;He et al, 2018). However, the Nympheae genus was not determined to exhibit monophyly, with the nested sister pairs of Victoria and Euryale, forming a sister group to that of the Hydrocallis and The workflow for orthogroups identification, filtering to improve phylogenetic signals and procedures to identify signals from multi-copy of orthologous gene sets for hybridization event detection.…”

“…Lotos subgenera, which first diverged in Nymphaea (López-Caamal and Tovar-Sánchez, 2014). The limited sampling in previous plastid phylogenetic studies resulted in Victoria and Euryale being nested into the genus Nymphaea (Gruenstaeudl et al, 2017;He et al, 2018). The combination of Victoria and Euryale formed a sister group with Nympheae jamesoniana.…”

“…The combination of Victoria and Euryale formed a sister group with Nympheae jamesoniana. (Gruenstaeudl et al, 2017;He et al, 2018). Nymphaea species are widely distributed into five subgenera, with three subgenera, including Nymphaea, Anecphya, and Brachyceras, diverging successively.…”