Wu P et al. (2022), The adaptive evolution of Euryale ferox to the ...

ECB-ART-50463

Plant J 2022 May 01;1103:627-645. doi: 10.1111/tpj.15717.

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The adaptive evolution of Euryale ferox to the aquatic environment through paleo-hexaploidization.

Wu P , Zhang L , Zhang K , Yin Y , Liu A , Zhu Y , Fu Y , Sun F , Zhao S , Feng K , Xu X , Chen X , Cheng F , Li L .

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Occupation of living space is one of the main driving forces of adaptive evolution, especially for aquatic plants whose leaves float on the water surface and thus have limited living space. Euryale ferox, from the angiosperm basal family Nymphaeaceae, develops large, rapidly expanding leaves to compete for space on the water surface. Microscopic observation found that the cell proliferation of leaves is almost completed underwater, while the cell expansion occurs rapidly after they grow above water. To explore the mechanism underlying the specific development of leaves, we performed sequences assembly and analyzed the genome and transcriptome dynamics of E. ferox. Through reconstruction of the three sub-genomes generated from the paleo-hexaploidization event in E. ferox, we revealed that one sub-genome was phylogenetically closer to Victoria cruziana, which also exhibits gigantic floating leaves. Further analysis revealed that while all three sub-genomes promoted the evolution of the specific leaf development in E. ferox, the genes from the sub-genome closer to V. cruziana contributed more to this adaptive evolution. Moreover, we found that genes involved in cell proliferation and expansion, photosynthesis, and energy transportation were over-retained and showed strong expression association with the leaf development stages, such as the expression divergence of SWEET orthologs as energy uploaders and unloaders in the sink and source leaf organs of E. ferox. These findings provide novel insights into the genome evolution through polyploidization, as well as the adaptive evolution regarding the leaf development accomplished through biased gene retention and expression sub-functionalization of multi-copy genes in E. ferox.

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	Figure 1. The dissection of the ancestral genome evolution of Euryale ferox.(a) Dot‐plotting of syntenic genes between the genomes of E. ferox and Nymphaea colorata. The dotted red lines indicate the break points in syntenic fragments of E. ferox genome compared with that of N. colorata; the rectangles of the same color indicate that these fragments are associated with each other in the diploid ancestral genome of E. ferox.(b) The karyotype of the diploid ancestral genome of E. ferox. The numbers on the bars are the IDs of corresponding genomic blocks (GBs).(c) Phylogenetic tree of four Nymphaeaceae species and the three E. ferox sub‐genomes, as well as two species, Ginkgo biloba and Amborella trichopoda, that were used as outgroups.(d) Frequency distribution of K s values between orthologous genes of pairwise genomes/sub‐genomes.(e) Pattern diagram of the two‐step process for the hexaploidization of E. ferox. [Colour figure can be viewed at wileyonlinelibrary.com]
	Figure 2. The separation of the three sub‐genomes in Euryale ferox.Boxplots of K s values on syntenic genes between Nymphaea colorata and E. ferox (a), as well as between N. colorata and E. ferox (b) for each ancestral karyotype of E. ferox (AKE) chromosome (AKEC). Variance tests were performed with * denoting P < 0.05 and ** denoting P < 0.01. The six candidate topologies of the phylogenetic tree, with the three topologies in (c) showing the phylogenetic tree on syntenic genes between the three sub‐genomes of E. ferox and the genome of N. colorata, as well as the pie diagrams for the corresponding tree (the same color) on the left. The three trees in (d) show the phylogenetic tree on orthologous genes between the three sub‐genomes of E. ferox and the genome of Victoria cruziana, as well as the pie diagrams for the corresponding tree. [Colour figure can be viewed at wileyonlinelibrary.com]
	Figure 3. The main development process and cytological observations of Euryale ferox leaves.(a) Different development stages of E. ferox leaves.(b) The E. ferox early adult leaves (EA1 and EA4) and adult leaves (A2, A4, and A7).(c) The paraffin sections (PS) of E. ferox early adult leaves (EA1 and EA4) and adult leaves (A2, A4 and A7). Differently colored bars denote the different parts of the leaf; photos inside the ellipse are the enlarged threefold views of the palisade and lower epidermis. [Colour figure can be viewed at wileyonlinelibrary.com]
	Figure 4. Expression atlases of Euryale ferox leaves in different developmental stages and other organs.(a) Expression profiles of sample‐specific genes in E. ferox. Genes are listed along the y‐axis; samples are listed along the x‐axis. The numbers at the bottom of the x‐axis indicate the number of sample‐specific genes in each sample. Bars on the left of the heatmap show the sample‐specific genes, which correspond to the samples in the same colors on the bottom of the x‐axis.(b) The heatmap shows the enrichment levels of sample‐specific genes and ubiquitous genes (y‐axis) in different sets of genes as listed in the x‐axis; one, two and three represent the copy number of polyploidized genes; Sub1, Sub2 and Sub3 represent the sub‐genomes to which the genes belong.(c) The average expression level of differentially expressed genes (DEGs) related to photosynthesis between early adult and adult leaves.(d) The morphology of adult and early adult leaves of E. ferox. EA1–EA4 are early adult leaves; A1–A3 are adult leaves underwater; A4 is the adult leaf just rising from the water; and A5–A7 are leaves above‐water.(e) The average expression level of DEGs related to cell proliferation between early adult and adult leaves. [Colour figure can be viewed at wileyonlinelibrary.com]
	Figure 5. Gene families associated with the specific development of leaves in Euryale ferox.(a) The expansion of gene families related to cell expansion and division in E. ferox, compared with that in Nymphaea colorata and Arabidopsis.(b) Phylogenetic tree of GRF genes in E. ferox, N. colorata and Arabidopsis. Red denotes E. ferox genes, green denotes N. colorata genes, and gray denotes Arabidopsis genes.(c) Comparisons of the number of ribosomal protein (RP) gene families in Ginkgo biloba (Gb), Amborella trichopoda (Atr), N. colorata (Nc), E. ferox (Ef), Oryza sativa (Os), Zea mays (Zm), Nelumbo nucifera (Nn), Vitis vinifera (Vv) and Arabidopsis (Ath).(d) Ratio of the number of RP genes to the number of total genes in the corresponding genome.(e) Expression atlases of SWEET genes in the leaves of different developmental stages and other organs of E. ferox. [Colour figure can be viewed at wileyonlinelibrary.com]
	Figure 6. The model of coordinated gene pathways underlying the adaptive evolution of specific strategy in Euryale ferox leaf development.There are five main gene pathways involved in the leaf development of E. ferox. (i) Photosynthesis. Early adult leaves and adult leaves above water provide the energy for the development of adult leaves underwater through SWEET genes. (ii) Cell proliferation. This process occurs and is completed at the underwater development stage of adult leaves, which lays the foundation for rapid expansion of leaves after they rise above the water. (iii) Cell expansion. The high expression of cell expansion‐related genes occurs at the underwater stage, and is completed at the above‐water stage. (iv) Phytohormones and (v) ribosome proteins (RPs). These genes are related to different phytohormones (Auxin, GA, Br and CK) and RPs that are involved in leaf development and occur at the underwater stage of adult leaves. These genes were over‐retained through paleo‐hexaploidization and became involved in the regulation of E. ferox leaf development. Different sizes of circles represent the copy number of genes. LHC, light‐harvesting chlorophyll a/b‐binding; PRK, phosphoribulokinase; GAPDH, glyceraldehyde‐3‐phosphate dehydrogenase; PGK, phosphoglycerate kinase; APC10, anaphase promoting complex10; GIF, grf‐interacting factor; CDC27, cell division cycle protein 27; TCP, teosinte branched1/cycloidea/pcf; GRF, growth‐regulating factor; ANT, aintegumenta; AIL, aintegumenta‐like1; CYCD3, cyclin d3; EOD1, enhancer of da1‐1; ARF, auxin response factor; KLU, kluh; EXP, expansin; EBP1, eRBb‐3 epidermal growth factor receptor binding protein; RPT2a, regulatory particle aaa‐atpase 2a; TOR, target of rapamycin; ZHD, zinc finger homeodomain; BR, brassinosteroids; GA, gibberellins; HK, histidine kinase; CK, cytokinin. [Colour figure can be viewed at wileyonlinelibrary.com]

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