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Tropical Plants 2023, 2:1
Water lily research: Past, present, and future
Xianghui Xiong1,2, Ji Zhang1,2, Yongzhi Yang3, Yuchu Chen4, Qun Su5, Ying Zhao6, Jian Wang6, Zhiqiang Xia1,2,
Liangsheng Wang7*, Liangsheng Zhang8* and Fei Chen1,2*
1Sanya Nanfan Research Institute and college of tropical crops, Hainan University, Sanya 572025, China
2Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
3Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
4Zhejiang Humanities Landscape Co., Ltd., Hangzhou 310000, Zhejiang, China
5Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
6College of Forestry, Hainan University, Haikou 570228, China
7Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
8College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310030, China
* Corresponding authors, E-mail: wanglsh@ibcas.ac.cn; fafuzhang@163.com; feichen@hainanu.edu.cn
Abstract
The water lily order Nymphaeales includes ~100 species and all grow into aquatic herbs. Most of them are not only economic crops but have, for
thousands of years, been regarded as cultural symbols, especially in Buddhism and Hinduism. Water lily order forms an early angiosperm branch,
occupying vital roles in evolutionary biology. With the advent and rapid development of omic techniques and bioinformatic software, the
research on water lily biology has achieved unprecedented success. In this review, we summarized a series of recent and important findings in
water lily research. Genomic analyses of water lilies provide insights into details of their evolutionary history and ecological adaptation. The
genomes also provide rich resources for genetic studies and molecular breeding. The opening and closing rhythm of flowering is controlled by
auxin and the candidate genes are proposed. Part of the genes responsible for floral scents and floral colors in Nymphaea colorata have been
studied in-depth for their functions. Metabolomic profiling reveals the anthocyanins responsible for the floral color formation and the volatile
organic compounds as floral scent molecules. Phenotypic studies surveyed the diverse traits from flowers to leaves and bulb roots, and some of
these studies reveal the link between genes and phenotypes. However, genes responsible for some critical traits such as the growth of water lily
plants, such as the stem, bulb formation, and the initiation of vivipary are still unknown. Finally, we propose potential future research of water
lilies, including genetics, breeding, and industrialization.
Citation: Xiong X, Zhang J, Yang Y, Chen Y, Su Q, et al. 2023. Water lily research: Past, present, and future. Tropical Plants 2:1
https://doi.org/10.48130/TP-2023-0001
Introduction
The Nymphaeales order, including three families
(Hydatellaceae, Cabombaceae, Nymphaeaceae) and 85 species
(Fig. 1), are called the water lily order[1,2], partly due to the
dominant character of all these species are aquatic herbs and
nearly all of the species have very beautiful flowers and leaves.
Hence the water lily is recognized as the common name for all
species categorized in the Nymphaeales order[3−8]. Water lilies
are globally distributed, spanning from tropical to cold
regions[9]. They have played vital roles in the economy, ecology,
and evolutionary biology.
Economic, cultural, ecological, and evolutionary values
of water lilies
Water lilies contain various economic values. The Nymphaea
spp. flowers are not only good cut flowers, but can be in food
and beverages[11]. For example, some Nymphaea water lilies
have starchy and edible roots[12]. The seeds of Victoria and
Euryale ferox are edible[13]. Nymphaea species contain various
medicinal compounds, and they have been found to function
in anti-bacteria[14], anti-inflammatory[15], and anti-depressant[16]
capacaties. According to data from the China Flower
Association, at the end of 2019, the annual output of water lilies
in China was 152 million heads, and the combined market size
of the lotus and water lily industries reached 10 billion CNY
(www.cqla.cn/chinese/news/news_view.asp?id=58006). In
Lichuan county from Hubei province, China, the 'hometown of
E. ferox in China', its planting area is about 2,000 hectares, and
the annual output value exceeds 200 million CNY
(http://news.yuanlin.com/detail/2021128/379540.htm). Water
lilies have high cultural value and a long consumption history.
In ancient Greece and Rome, together with the lotus, some
Nymphaea species were regarded as the embodiment of
holiness and beauty and were often used as offerings to the
gods. In modern times, one of the top impressionist painters
Claude Monet has painted hundreds of water lilies[17]. Many
countries have issued stamps or currency with water lily flowers
as the theme. Water lilies have a certain ecological value,
especially in water purification and heavy metal absorption[18].
However, some Nymphaea species grow very quickly and are
regarded as invasive species. For example, N. odorata and N.
capensis encroach heavily on the living space of other species
in the same ecosystem and destroy the ecological balance
(www.invasive.org/species/aquatic.cfm and www.issg.org/
database/species/ecology.asp?si=985&lang=SC.)
REVIEW
© The Author(s)
www.maxapress.com/tp
www.maxapress.com
The water lily order occupies a critical evolutionary position.
Together with Amborellales and Austrobaileyales, these three
orders collectively form the ANA (Amborellales-Nymphaeales-
Austrobaileyales) grade, which are the first three flowering
plant branches[19]. The early diverging water lily order provides
a unique window to study the origin and early evolutionary
features of flowering plants. Besides, the various kinds of floral
scents and colors are wonderful traits for ornamental studies.
Their genes and related pathways are the focus of the
molecular breeding of water lilies and even other ornamental
plants.
Growing research on water lilies
Multi-omic tools, including genomics, epigenomics, transcrip-
tomics, proteomics, and metabolomics, are high-throughput
and effective tools for plant studies. With the development of
high-throughput technologies and bioinformatics tools,
various omic research continues to deepen our understanding
of plant traits[20]. Through high-throughput measurement of
each omics and data integration, we can not only compre-
hensively and systematically understand gene functions and
promote molecular breeding, but also provide important data
and technical approaches for the research of emerging cross
disciplines such as quantitative and systems biology.
To date, there are roughly 868 publications indexed in the
PubMed database (Fig. 2). The annual number grows rapidly,
from eight publications in 2000 to 71 in 2021. The rapid
increase reveals the boosted interest in various kinds of water
lilies, from Nymphaea to others.
Genome sequences of three water lilies
The genome sequence of Nymphaea colorata
Chen et al. selected the N. colorata, a diploid tropical species
that originated from east Africa for genome sequencing due to
its relatively small genome size and small plant size[21]. Relying
on the PacBio long-read sequencing technology, a 409 Mb
genome is assembled, falling into 14 chromosomes[9]. The
genome assembly has relatively high quality with contig N50
up to 2.1 Mb. Besides, some telomeres and centromeres are
very well assembled and characterized. At the same time, the
genomes of its mitochondria and chloroplast are successfully
assembled using the same PacBio reads[22]. Based on its
genome information, we are able to precisely reveal its
evolutionary place (Fig. 3) and identify the genes responsible
for the floral scent, floral color[23], as well as floral
morphogenesis[24]. The expansion of biotic and abiotic stress-
related genes such as WRKY genes and R genes is related to the
wide distribution of the Nymphaea water lilies[25]. Some of the
key genes responsible for the stomata development are lost in
the N. colorata genome and may explain its unique aquatic
lifestyle adaptation[26]. This is the first report on the water lily
genome sequence, which is a milestone showing that water lily
research is entering the genomic era.
The genome sequence of N. thermarum
Povilus and colleagues from Harvard University assembled a
draft genome of a dwarf tropical water lily N. thermarum[27].
This species originates from Rwanda (east Africa). Relying on
Illumina short reading sequencing technology, they obtained a
a b
c
Fig. 1 The evolutionary position of water lilies. (a) Tree of green plant lineage. (b) Tree of angiosperms (flowering plants). (c) Tree of water lily
order Nymphaeales. Phylogenetic relationships and timing of the nodes are based on previous phylogenomic research[9] and
phylotranscriptomic research[10].
Water lily research: Past, present, and future
Page 2 of 8 Xiong et al. Tropical Plants 2023, 2:1
368 Mb genome of N. thermarum. Analyses of this genome and
phenotypes reveal the loss of genes enrolled in the vascular
cambium, which might be a key innovation of its adaptation to
the aquatic environment. This is the second report on the water
lily genome.
The genome sequence of Euryale ferox
The Euryale genus only contains one species (E. ferox) which
is mainly distributed in southern and eastern Asia. Their leaves
and flowers are covered in sharp prickles and float on the
water’s surface. Its edible seeds are usually called fox nuts and
are used as food or diet therapy supplies in Asia. Relying on the
long-read sequencing platform Oxford Nanopore Technology,
Liu and colleagues assembled the genome sequence of E.
ferox[28]. The genome assembly has a size of 725.2 Mb and 29
chromosomes. Phylogenomic studies also support that E. ferox
is an early angiosperm branch, following the Amborella, and the
incomplete lineage sorting may largely account for phyloge-
netic inconsistencies of different major lineages in
angiosperms. This is the third report on the water lily genome,
which provides important resources to reveal the specific
evolution of seeds and leaves.
Whole-genome methylation researches
There has been little focus on the DNA methylation in water
lily research. Bisulfite sequencing (BS-seq) on Nuphar advena
did not find CHH type methylation in its genome. Comparative
analyses of N. advena and other land plants’ relative levels of
CG methylation are a consistent property across genes, and
genic CHG methylation correlates with genome size[29]. We
believe that in the future, more results will emerge as more
genome sequences of water lilies become available.
Floral development
Flowering time
Most Nymphaea species bloom in the morning and close
their flowers in the afternoon. Only a few species bloom at
night and close their flowers before the morning. This unique
circadian flowering clock is very interesting and attractive.
Chen et al. collected flower samples at different time points
and sequenced the transcripts[30]. They uncovered eight expre-
ssional gene clusters related to floral circadia. They showed that
auxin-related signaling pathway genes are linked to synchro-
nized expression patterns with opening and closure processes.
The bloom of Nymphaea flowers usually last three to four
days, which largely shortens the shelf life of cut flowers. Li et al.
investigated when the senescence process is initiated and how
it terminates the movement rhythm[31]. They identified multiple
signaling pathways that were activated at the last stage, the
floral closure, on the third day after flowering. Genes related to
hydrolase are upregulated on the same day, indicating that
petals enter the senescence stage at that time.
Fig. 2 The growing research publications on water lilies. The searches are based on PubMed from NCBI (https://pubmed.ncbi.nlm.nih.gov/)
on May 24, 2022. Count 1 shows the keywords '(nymphaea) OR (waterlily) OR (water lily) OR (euryale) OR (barclaya) OR (nuphar) OR (trithuria)
OR (cabomba) OR (brasenia)', while count 2 shows the keywords 'nymphaea'.
Fig. 3 Schematic diagram showing that the phylogenomic
analyses reveal accurate phylogeny of angiosperms. Tree A
represents that Nymphaeales, but not Amborellales forms the
earliest extant angiosperm branch. Tree B represents Amborellales
as the earliest extant angiosperm branch. Tree C represents
Amborellales and Nymphaeales are sister lineage as the co-first
earliest extant angiosperm branch. The proportion data in the
piechart are from our previously published article[9]. E: Eudicots, M:
Monocots, Au: Austrobaileyales, Am: Amborellales, N:
Nymphaeales.
Water lily research: Past, present, and future
Xiong et al. Tropical Plants 2023, 2:1 Page 3 of 8
Floral fragrance
Unlike species from the Hydatellaceae family and
Cabombaceae family, most Nymphaea flowers emit fragrant
molecules, volatile organic compounds, to attract various kinds
of pollinators. A wide variety of small molecules or metabolites
are responsible for the diverse floral colors and scents.
Identifying small molecules using gas chromatography-mass
spectrometry (GC-MS) is becoming more common. For
example, GC-MS-based screening on the flower petals of N.
nouchali identified 16 biologically active phytochemicals[32].
GC-MS on the N. pubescens’s crude pedicel and flower also
identified 45 bioactive compounds[33]. However, another study
using the same method on the flower of N. pubescens identified
71 bioactive compounds[34]. A total of 22 VOCs were found in
the seven species of Nymphaea subgenus Hydrocallis[35]. Gas-
liquid chromatography (GLC) based extraction of N. alba leaf
identified 53 bioactive compounds[36]. The ultra-performance
liquid chromatography-tandem mass spectrometry (UPLC-
MS/MS) screen on the flower of N. ‘Blue Bird’ identified 455
metabolites[37]. A large-scale screen on 56 water lily cultivars
identified 117 volatile organic compounds (VOCs), in which
alkenes and alkanes were the most abundant, followed by
ketones and aldehydes[38]. The N. colorata flower releases 11
different volatile molecules, mainly terpenoids, fatty acids, and
benzenoids as fragrant molecules, among which methyl
decanoate is the major fragrance molecule[9] (Fig. 4).
The Victoria genus only includes species V. amazonica, V.
cruziana, and the recently identified species V. boliviana[39].
Exploration of floral scent composition using GC-MS could
provide a large array of floral VOCs in a series of water lilies. In
Victoria cruziana, four VOCs were identified from its flower, in
which the VOC composition and emission time are also
identified[40].
At the genetic level, transcriptome analyses identified a
SABATH gene family member, NC11G0120830, and a terpene
synthase gene family member, NC11G0123420, as highly and
uniquely expressed in petals and involved in the metabolism of
fragrant molecules[9].
Floral colors
Nymphaea species display a variety of floral petal colors,
including white, red, purple, yellow, blue, etc. A few Nymphaea
water lilies, such as N. colorata, N. caerulea, N. 'King of Siam', etc.,
exhibit beautiful blue petals. Flavonoids are the key elements
of floral color. Nymphaea species contain a wide variety of
flavonoids. For example, a broad sampling of 35 tropical
Nymphaea cultivars identified 34 flavonoids[41]. Transcriptome
sequencing was conducted on the colorless stage and the fully
colored stage of the blue flower cultivar N. 'King of Siam'.
Although no reference genome was available for this species,
Wu et al.[42] still identified 26,206 unigenes, among which 1,581
genes have differential expression values between the two
stages. An in-depth survey revealed that 33 genes with sig-
nificant expressional levels are responsible for color formation.
Finally, the authors validated the expressional changes of seven
ANTHOCYANIDIN 3-O GLUCOSYLTRANSFERASE (UA3GT) genes
using the qRT-PCR method[42]. N. colorata has very attractive
blue petals. Zhang et al.[9] have identified the
Dp3′galloylacetylGal as the main anthocyanin for blue
coloration in the petals (Fig. 4).
The Victoria species display large flowers, showing white
petals on the first day, turning pink or red on the second day.
Relying on the combination method of high-performance
liquid chromatography with photodiode array detection (HPLC-
DAD) and ultra-performance liquid chromatography coupled
with tandem mass spectrometry (UPLC-MS/MS), Wu et al.
identified 14 flavonoids, including 10 flavonols and four
anthocyanins, in the petals of two Victoria species[43].
Seed biology
The large and starchy seeds of E. ferox are both a nutritious
food and a medicine in East Asia. By transcriptomic analyses of
different seed stages, Liu et al. found increased expression of
P450 and PAL genes in phenylpropanoid metabolism, which
might be involved in the maturation of its seeds in aspects of
seed size, color, harness, and accumulation of secondary
metabolites[13]. Specifically, the authors found the changed
expressional pattern of flavonoids during the seed develop-
ment, involving ABA and SA phytohormones. Candidate genes
in regulating the two phytohormones in regulating the
flavonoids are identified[44].
Leaf vivipary: rapid vegetative propagation
strategy by tropical water lilies
Some Nymphaea species are leaf vivipary by producing
seedlings on the leaves. As an interesting horticultural trait, the
leaf vivipary is not only a supplement to breeding programs,
but also an opportunity to study stem cell initiation in mature
organs. By comparing the transcriptomes of four stages of leaf
development between the non-vivipary N. colorata and the
vivipary N. micrantha, Su et al. found four potential regulators,
including the transcription factors ERF1B, ERF105, RAP2-3, and
WRKY22[45]. In the future, through functional studies of genes,
such as CRISPR-Cas9 mediated gene knockout and transgenic
technologies, it is possible to gain more knowledge of the
origin and evolution of vivipary in plants.
Floral vivipary: branching flowers
Nymphaea prolifera is the water lily currently known to
produce floral vivipary, an amazing trait called branching
flowers. Instead of fertile flowers, N. prolifera usually produces
tuberiferous and sterile flowers that act as vegetative organs. N.
prolifera can produce two levels and sometimes even three
levels of branching flowers, giving rise to dozens and often
more than 100 vegetative propagules[46]. This unique trait is,
however, still under researched. In the future, its potential in
general biology will perhaps show its significance, at least in
breeding or maintaining important mutations.
The water lily rhizome and tuber bulb
A large number of angiosperm crops, including the Allium,
Iris, Tulipa, and Begonia, have bulbs. All Nymphaeaceae species
contain starchy tuber bulbs, although ranging dramatically in
size from one centimeter to a foot. It seems that the bulbs have
evolved independently many times during evolution.
Nymphaea water lilies develop four major types of bulbs,
including Marliac-type rhizome, pineapple-type rhizome,
ordorata-type rhizome, and tuberosa-type rhizome. These
bulbs are rich in starch and nutrients, making them a good
alternative food in some tropical regions. At the genetic level,
Water lily research: Past, present, and future
Page 4 of 8 Xiong et al. Tropical Plants 2023, 2:1
a
c d
b
Fig. 4 (a) Phenomics, (b) genomics, (c) metabolomics, and (d) transcriptomics, guided gene screening related to blue anthocyanin in the petal
of N. colorata and the stomata development. The genomic and phenomic studies identified loss of genes associated with stomatal
development in the lower abaxial side leaf of N. colorata. Genomic, transcriptomic, and metabolomic studies identified floral fragrance-related
genes and pathways associated with blue anthocyanin synthesis.
Water lily research: Past, present, and future
Xiong et al. Tropical Plants 2023, 2:1 Page 5 of 8
the FLOWERING LOCUS T (FT) genes are found to be involved in
bulb formation in onions[47]. Zhang et al. found a total of five FT
genes in the genome of Nymphaea colorata[9]. The five FT genes
are clustered into two groups, which are produced by Pi-whole
genome duplication[48]. This suggests that the two groups may
have different functions, with one group controlling the
flowering time and the other controlling the bulb formation.
However, due to the very limited research on water lilies, we
still do not know which FT gene is responsible for its bulb
initiation and development.
The runner stem in water lilies
A few water lily species produce stems that grow flat along
the ground called runners. It will root at the node and form a
new plant, thereby spread rapidly. The Nymphaea mexicana
and the Brasenia schrebri produce runners and become an
invasive species in many aquatic environments. The runner is
also common in monocot plants such as wild rice and Iris spp.,
and eudicots such as strawberry and fish mint. Runners could
be utilized for plant propagation. Although we now know that
the phytohormone GA and the DELLA gene are involved in
runner formation[49], the genetics of the runner is completely
unknown in water lilies.
Germplasm studies
Hybrid breeding within and across various Nymphaea species
is relatively easy and popular. To date, there are hundreds of
Nymphaea cultivars available. Different Nymphaea cultivars
display various floral colors, floral scents, flowering times, leaf
shapes, and bulb sizes. Various traits of water lily populations
have been collected for a long time and many of them have
been well described and statistically analyzed. Dąbrowska et al.
studied nine traits, including leaf length, length of outer petals,
and maximum leaf width, of four Nymphaea species[50]. Pan et
al. collected 86 Nymphaea cultivars and 45 traits. These traits
include floral colors, length of the leafstalk, leaf size, bud shape,
and bulb shape. Results show that extensive variations occur in
this population, in which floral color is the most highly diverse
trait[51].
Xu et al. find that Nymphaea species have an asymmetrical
distribution of stomata on the leaf, with normal stomata on the
adaxial side and abnormal ones on the abaxial side. Relying on
the reference genome sequence of N. colorata, a series of core
stomata regulators, including EPF2, AP2C3, MPK6, as well as
stomatal polarity regulators BASL and POLAR genes, are absent
in its genome, indicating that gene loss is a major innovation in
its aquatic adaptation. This study provides an example that
gene linkage phenotype analyses could be a trend in future
studies[26].
Water lilies are promising model plants for
studying plant evolution and floral biology
Water lilies have some advantageous characteristics as
potential model plants for genetic and genomic studies (Fig. 5).
All water lilies grow into aquatic herbs, and most Nymphaea
water lilies have small sizes, with some species even stretching
up to 0.5 m in diameter. Some Nymphaea water lilies (i) have
rapid life (around three to four months from seed to seed), and
bloom all the year in tropical regions, (ii) have lots of flowers in
a single plant and each flower contains ~3,000 fertile seeds.
These characteristics make them ideal candidates for model
plants. In addition, the release of the genome sequence of N.
colorata, together with the genetic transformation pipeline of
Nymphaea species[4], all allow Nymphaea water lilies to be ideal
model plants for studying the evolution of angiosperms and
floral characteristics.
Cabomba plants also have some excellent traits and growth
characteristics, suitable as model plants for studying the origin
of angiosperms. For example, C. aquatica and C. caroliniana can
be efficiently cultivated in the laboratory[52]. Their flowering can
be induced by light, and their small size as an aquatic herb with
a smaller than average genome of the ANA grade, all make
Cabomba a suitable model plant[52].
Trithuria, a small genus with 12 species from Australia, New
Zealand, and India, grows to very a small size (~2 cm in height)
and flowers very quickly in the laboratory[53]. Its seeds can be
stored conveniently[53]. In summary, Trithuria spp. may provide
a good opportunity for both reverse and forward genetic
screening.
Future development of water lily studies
Combination of omic tools and bioinformatic
techniques
The water lily order contains about 100 species with a
relatively wide geographical distribution, and different species
possess a large number of different metabolites. In the future,
multi-omic tools will be combined in water lily research.
Eventually, all water lily genome sequences will be deciphered
by relying on long-length or even ultra-long read-length
sequencing technology with high accuracy. Based on this, the
micro-evolution of all water lilies will be deeply revealed, such
as more phenotypically related genes can be mined using
genome-wide association studies (GWAS) technology. Using
epigenomic technology, we can deepen our understanding of
gene regulation. More metabolites can be mined using
metabolomics, while the association between genes and
phenotypes can be studied by phenomics. In conclusion, more
Fig. 5 The life cycle and characteristics of Nymphaea water lily
make it a suitable model plant. Genetic transformation through its
flowers is available in water lilies, similar to that in Arabidopsis. The
numerous seeds in one Nymphaea fruit pod provide a good
opportunity for the construction of a mutant library. By laboratory
culture of seeds or organs, water lily could be ideal for lab
research. Batch culture of water lilies is relatively easy as shown in
the illustration.
Water lily research: Past, present, and future
Page 6 of 8 Xiong et al. Tropical Plants 2023, 2:1
and more technologies will contribute significantly to the
understanding and application of water lilies.
From genetics to breeding and industry
In the near future, we are confident that all water lily
genomes will be decoded (Fig. 6). The pan-genome of water
lilies will be established. Genome-wide association studies and
genome editing will accelerate the genetics of water lilies. The
various genes and pathways responsible for important traits
will be uncovered. Afterward, these genes will be employed for
intelligent molecular design breeding. Excellent varieties of
water lilies will emerge, coupled with large-scale cultivation for
application in the water lily industry.
Acknowledgments
The authors acknowledge the funding from the National
Natural Science Foundation of China (32172614) and a startup
fund from Hainan University.
Conflict of interest
Fei Chen, Zhiqiang Xia, and Liangsheng Zhang are the
Editorial Board members of Journal Tropical Plants. They were
blinded from reviewing or making decisions on the manuscript.
The article was subject to the journal's standard procedures,
with peer-review handled independently of these Editorial
Board members and their research groups.
Dates
Received 20 June 2022; Accepted 13 December 2022;
Published online 30 January 2023
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