Water lilies as emerging models for Darwin’s abominable mystery

Fei Chen , Xing Liu , Cuiwei Yu , Yuchu Chen , Haibao Tang , Liangsheng Zhang

Horticulture Research ›› 2017, Vol. 4 ›› Issue (1) : 17051

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Horticulture Research ›› 2017, Vol. 4 ›› Issue (1) :17051 DOI: 10.1038/hortres.2017.51
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Water lilies as emerging models for Darwin’s abominable mystery
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Abstract

Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants. The birth and rapid radiation of flowering plants has interested many scientists and was considered ‘an abominable mystery’ by Charles Darwin. In searching for the angiosperm evolutionary origin and its underlying mechanisms, the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages; however, little is known regarding the genetics and genomics of another basal angiosperm lineage, namely, the water lily. In this study, we reviewed current molecular research and note that water lily research has entered the genomic era. We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin’s ‘abominable mystery’. Four pantropical water lilies, especially the recently sequenced Nymphaea colorata, have characteristics such as small size, rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms. The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.

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Fei Chen, Xing Liu, Cuiwei Yu, Yuchu Chen, Haibao Tang, Liangsheng Zhang. Water lilies as emerging models for Darwin’s abominable mystery. Horticulture Research, 2017, 4 (1) : 17051 DOI:10.1038/hortres.2017.51

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References

[1]

Raja MKMM, Sethiya NK, Mishra SH . A comprehensive review on Nymphaea stellata: a traditionally used bitter. J Adv Pharm Technol Res 2010; 1: 311-319.

[2]

Tani M, Sawada A, Oyabu T, Seiryo K . Ability of water lilies to purify water polluted by soap and their application in domestic sewage disposal facilities. Sens Mater 2006; 18: 91-101.

[3]

Friedman WE . Hydatellaceae are water lilies with gymnospermous tendencies. Nature 2008; 453: 94-97.

[4]

Biswal DK, Debnath M, Kumar S, Tandon P . Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding. BMC Bioinformatics 2012; 13: S26.

[5]

Les DH, Schneider EL, Padgett DJ, Soltis PS, Soltis DE, Zanis M . Phylogeny, classification and floral evolution of water lilies (Nymphaeaceae; Nymphaeales): a synthesis of non-molecular rbcL, matK, and 18S rDNA data. Syst Bot 1999; 24: 28-46.

[6]

Gandolfo MA, Nixon KC, Crepet WL . Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early angiosperms. Proc Natl Acad Sci USA 2004; 101: 8056-8060.

[7]

Soltis D, Soltis P, Nickrent D et al. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann Miss Bot Gard 2015; 71: 607-630.

[8]

Qiu Y, Lee J, Bernasconi-quadroni F, Zimmer EA, Chen Z, Savolainen V . The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 1999; 402: 404-407.

[9]

Zeng L, Zhang Q, Sun R, Kong H, Zhang N, Ma H . Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun 2014; 5: 4956.

[10]

Wickett NJ, Mirarab S, Nguyen N et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci USA 2014; 111: E4859-E4868.

[11]

Drew BT, Ruhfel BR, Smith SA et al. Another look at the root of the angiosperms reveals a familiar tale. Syst Biol 2014; 63: 368-382.

[12]

Leebens-Mack J, Raubeson LA, Cui L et al. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one’s way out of the Felsenstein zone. Mol Bio Evol 2005; 22: 1948-1963.

[13]

Yang X, Tuskan GA, Tschaplinski TJ, Cheng Z-M. Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence. Nat Preced 2007, 1-20.

[14]

Simmons MP, Gatesy J . Coalescence vs. concatenation: sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015; 91: 98-122.

[15]

Goremykin VV, Nikiforova SV, Cavalieri D, Pindo DM, Lockhart P . The root of flowering plants and total evidence. Syst Biol 2015; 64: 879-891.

[16]

Diao Y, Chen L, Yang G et al. Nuclear DNA C-values in 12 species in Nymphaeales. Caryologia 2006; 59: 25-30.

[17]

Pellicer J, Kelly LJ, Magdalena C, Leitch IJ . Insights into the dynamics of genome size and chromosome evolution in the early diverging angiosperm lineage Nymphaeales (water lilies). Genome 2013; 56: 437-449.

[18]

Yamada T, Ito M, Kato M . Expression pattern of INNER NO OUTER homologue in Nymphaea (water lily family, Nymphaeaceae). Dev Genes Evol 2003; 213: 510-513.

[19]

Luo H, Chen S, Wan H, Chen F, Gu C, Liu Z . Candidate reference genes for gene expression studies in water lily. Anal Biochem 2010; 404: 100-102.

[20]

Luo H, Chen S, Jiang J et al. The expression of floral organ identity genes in contrasting water lily cultivars. Plant Cell Rep 2011; 30: 1909-1918.

[21]

Amborella Genome Project . The Amborella genome and the evolution of flowering plants. Science 2013; 342: 1241089.

[22]

Chaveerach A, Tanee T, Sudmoon R . Molecular identification and barcodes for the genus Nymphaea. Acta Biol Hungarica 2011; 62: 328-340.

[23]

Cui L, Wall PK, Leebens-mack JH et al. Widespread genome duplications throughout the history of flowering plants. Genome Res 2006; 16: 738-749.

[24]

Yoo MJ, Chanderbali AS, Altman NS, Soltis PS, Soltis DE . Evolutionary trends in the floral transcriptome: Insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae). Plant J 2010; 64: 687-698.

[25]

Wu Q, Wu J, Li S-S et al. Transcriptome sequencing and metabolite analysis for revealing the blue flower formation in waterlily. BMC Genomics 2016; 17: 897.

[26]

Friedman WE . The meaning of Darwin’s ‘abominable mystery’. Am J Bot 2009; 96: 5-21.

[27]

Soltis PS, Soltis DE, Chase MW . Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 1999; 402: 402-404.

[28]

Kuzoff RK, Gasser CS . Recent progress in reconstructing angiosperm phylogeny. Trends Plant Sci 2000; 5: 330-336.

[29]

Qiu Y, Dombrovska O, Lee J et al. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int J Plant Sci 2005; 166: 815-842.

[30]

Delsuc F, Brinkmann H, Philippe H . Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005; 6: 361-375.

[31]

Goremykin VV, Nikiforova SV, Biggs PJ et al. The evolutionary root of flowering plants. Syst Biol 2013; 62: 50-61.

[32]

Xi Z, Liu L, Rest JS, Davis CC . Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Syst Biol 2014; 63: 919-932.

[33]

Friedman WE . Embryological evidence for developmental lability during early angiosperm evolution. Nature 2006; 441: 337-340.

[34]

Carpenter KJ . Stomatal architecture and evolution in basal angiosperms. Am J Bot 2005; 92: 1596-1615.

[35]

Friis E, Pedersen K, Crane PR . Fossil evidence of water lilies (Nymphaeales) in the early cretaceous. Nature 2001; 410: 357-360.

[36]

Sang T. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit Rev Biochem Mol Biol 2002; 37: 121-147.

[37]

Betancur-R R, Naylor GJP, Ortí G . Conserved genes, sampling error, and phylogenomic inference. Syst Biol 2014; 0: 1-6.

[38]

Mirarab S, Bayzid MS, Boussau B, Warnow T . Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 2014; 346: 1250463.

[39]

Liu L, Edwards SV . Comment on ‘Statistical binning enables an accurate coalescent-based estimation of the avian tree’. Science 2014; 350: 171.

[40]

Springer MS, Gatesy J . The gene tree delusion. Mol Phytolgenet Evol 2016; 94: 1-33.

[41]

Edwards SV, Xi Z, Janke A et al. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Mol Phytolgenet Evol 2016; 94: 447-462.

[42]

Salichos L, Rokas A . Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 2013; 497: 327-331.

[43]

Burki F, Shalchian-Tabrizi K, Minge M et al. Phylogenomics reshuffles the eukaryotic supergroups. PLoS One 2007; 2: e790.

[44]

Prum RO, Berv JS, Dornburg A et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2015; 526: 569-573.

[45]

Ricardo B-R, Broughton RE, Wiley EO et al. The tree of life and a new classification of bony fishes. PLOS Curr Tree Life 2013, 1-52.

[46]

Zeng L, Zhang N, Zhang Q, Endress PK, Huang J, Ma H . Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytol 2017; 214: 1338-1354.

[47]

Vialette-Guiraud ACM, Alaux M, Legeai F et al. Cabomba as a model for studies of early angiosperm evolution. Ann Bot 2011; 108: 589-598.

[48]

Povilus RA, Losada JM, Friedman WE . Floral biology and ovule and seed ontogeny of Nymphaea thermarum, a water lily at the brink of extinction with potential as a model system for basal angiosperms. Ann Bot 2015; 115: 211-226.

[49]

VanBuren R, Bryant D, Edger PP et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 2015; 527: 508-511.

[50]

Buggs RJA . The deepening of Darwin’s abominable mystery. Nat Eco Evol 2017; 1: 169.

[51]

Herendeen PS, Friis EM, Pedersen KR, Crane PR . Palaeobotanical redux: revisiting the age of the angiosperms. Nat Plants 2017; 3: 17015.

[52]

Gaikward SP, Yadav SR . Further morphotaxonomical contribution to the understanding of the family Hydatellaceae. J Swamy Bot 2003; 20: 1-10.

[53]

Iles WJD, Rudall PJ, Sokoloff DD et al. Molecular phylogenetics of Hydatellaceae (Nymphaeales): sexual-system homoplasy and a new sectional classification. Am J Bot 2012; 99: 663-676.

[54]

Kynast RG, Joseph JA, Pellicer J, Ramsay MM, Rudall PJ . Chromosome behavior at the base of the angiosperm radiation: karyology of Trithuria submersa (Hydatellaceae, Nymphaeales). Am J Bot 2014; 101: 1447-1455.

[55]

Marques I, Montgomery SA, Barker MS et al. Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). New Phytol 2016; 210: 310-323.

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