Yang Y et al. (2020), Prickly waterlily and rigid hornwort genomes sh...

ECB-ART-48558

Nat Plants 2020 Mar 01;63:215-222. doi: 10.1038/s41477-020-0594-6.

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Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution.

Yang Y , Sun P , Lv L , Wang D , Ru D , Li Y , Ma T , Zhang L , Shen X , Meng F , Jiao B , Shan L , Liu M , Wang Q , Qin Z , Xi Z , Wang X , Davis CC , Liu J .

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Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2-5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species-prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)-and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.

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Fig. 1. Comparative genomics analyses.a, The genomic features of E. ferox (pseudomolecules size: 721.2 Mb) and C. demersum (pseudomolecules size: 703.8 Mb). From inside to outside: GC content in 500-bp sliding windows (i; minimum–maximum, 0.2–0.8); repeat density in 10-kb sliding windows (ii; minimum–maximum: 0–1.0, coloured from white to dark green); gene density in 100-kb sliding windows (iii; minimum–maximum, 0–30, coloured from white to dark orange); and SNV density in 100-kb sliding windows (iv; minimum–maximum: 0–0.025). The links in the centre connect syntenic gene blocks that were detected using MCscan. Chr, chromosome. b, Distribution of average synonymous substitution levels (Ks) between syntenic blocks after evolutionary rate correction. c, Syntenic blocks (involving ≥10 colinear genes) between genomes. The corresponding median Ks value is shown for each block, and polyploidization events are represented by different colours.

Fig. 2. Phylogenomic analyses of early-diverging angiosperms.a, Chronogram of early-diverging angiosperms on the basis of the dataset SSCG-CDS inferred using MCMCTree. Bootstrap support percentages and posterior probabilities are indicated for each internal branch (from left to right, SSCG-CDS concatenation analysis using maximum likelihood (CA-ML), SSCG-CDS ASTRAL, LCG-CDS STAG, SSCG-Codon12 CA-ML, SSCG-Codon12 ASTRAL, LCG-Codon12 STAG), and an asterisk indicates 100 bootstrap support percentages and 1.0 posterior probabilities in all analyses. i, ii and iii indicate each internal branch. C, Carboniferous; J, Jurassic; K, Cretaceous; N, Neogene; P, Permian; , Triassic; Q, Quaternary; , Palaeogene. b, Species tree analysis using DiscoVista. Rows correspond to focal splits, and the spectrum indicates the support value for splits that are compatible with a species tree. Teal indicates themonophyly of a clade, and the different shades of teal indicate the level of its bootstrap support percentage (0 to 100%). Orange indicates rejection of a clade, and a 95% cut-off (instead of astandard 75%) was selected for strong rejection due to higher support values with genome-scale data. c, Superimposed ultrametric gene trees in a consensus DensiTree plot. The datasets SSCG-CDS and SSCG-Codon12 are shown in red and orange, respectively. d, The frequency of three topologies (q1–q3) around focal internal branches of ASTRAL species trees in the datasets SSCG-CDS and SSCG-Codon12. Each internal branch (labelled i, ii and iii) with four neighbouring branches can lead to three possible topologies (for example, q1, q2 and q3). e, Gene tree compatibility. The portion of gene trees for which focal splits are highly (or weakly) supported (or rejected). Weakly rejected splits are those that are not in the tree but are compatible if low support branches (below 75%) are contracted.

References [+] :

Amborella Genome Project, The Amborella genome and the evolution of flowering plants. 2013, Pubmed