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Int J Mol Sci
2018 Nov 28;1912:. doi: 10.3390/ijms19123780.
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Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics.
He D
,
Gichira AW
,
Li Z
,
Nzei JM
,
Guo Y
,
Wang Q
,
Chen J
.
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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 been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. 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 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, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.
XDB31010000 the Strategic Priority Research Program of Chinese Academy of Sciences, 31570220 the National Natural Science Foundation of China, Y655261W03 Wuhan Botanical Garden, Chinese Academy of Sciences
Figure 1. Circular gene maps of five chloroplast genomes of Nymphaeaceae. Grey arrows indicate the direction in which genes are transcribed. Color codes indicates the various gene functional groups, and the grey-shaded part in the inner circle shows the GC level of each chloroplast genome.
Figure 2. Details of codon preferences (bar) and relative synonymous codon usage values (line) of 12 chloroplast genomes of Nymphaeaceae.
Figure 3. Number of RNA-editing sites in each of the transcripts of 19 common genes in all analyzed chloroplast genomes.
Figure 4. Comparison of the border positions of the large single copy, small single copy, and the inverted-repeat regions among chloroplast genomes of twelve species of Nymphaeaceae. Complete genes and portions of genes adjacent to the junctions are depicted by differently colored blocks.
Figure 5. Mauve software alignment of the whole chloroplast genome of 12 species of Nymphaeaceae. Local collinear blocks representing identical gene clusters are depicted by the same color and are connected by lines.
Figure 6. Phylogenetic relationships among the species of Nymphaeaceae, Cabombaceae, and Hydatellaceae (outgroup). The Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic tree was based on 66 protein codon genes. The numbers indicate ML bootstrap support (100) and BI posterior probabilities (1.0) values. The - symbol indicates maximum support. The first two values and the last two are for unpartitioned data and partitioned data respectively.
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