(except in nutrient-poor or highly acidic water). In
addition to its nutritional value and fast biomass
production, these plants can purify highly concentrated waste streams into safe drinking water.
Importantly, duckweed production can possibly
be scalable from households (e.g., 5 L tanks),
small garden or village ponds to severalhectare-sized wastewater lagoons. Provided that
duckweed is globally distributed, duckweedbased solutions can be available on all continents
but Antarctica (for review, see Cao et al. 2018).
Fascinatingly, duckweed was additionally described as one of the most attractive higher plants for
long-duration supporting human life in space
(Yuan and Xu 2017). However, the implementation of these multi-purpose plants has still been
underrated partly due to currently incomplete
knowledge on duckweed biology and agriculture.
The availability of high-quality duckweed
reference genome sequences has ushered in new
and detailed insights into the mechanisms
underpinning biological processes of these
aquatic, highly morphologically reduced plant
models. The first duckweed genome Spirodela
polyrhiza (aka., the Greater Duckweed), chosen
due to its basal phylogenetic position and
smallest genome size, was sequenced by an
international consortium led by scientists from
Rutgers University (Wang et al. 2014). This
high-quality reference genome was improved to
the chromosome-level assembly by using
multi-color fluorescence in situ hybridization
(Cao et al. 2016a), optical mapping (Michael
et al. 2017), and Oxford Nanopore Technology
sequencing of another ecotype (aka., clone 9509)
of the same species (Hoang et al. 2018). Since
publication in 2014, the Spirodela genome has
been cited more than 100 times on the Google
Scholar indexing platform (dated July 2019),
serving as a duckweed reference genome not
only for greatly facilitating duckweed genomic
investigation (e.g., MAD box genes by Gramzow
and Theissen 2015; pentatricopeptide-repeat
proteins by Wang et al. 2016) but also for comparative genome analysis of other monocot and
aquatic plants (e.g., seagrass for angiosperm
adaptation to the sea by Olsen et al. 2016).
18.2 Future Prospects in Duckweed
Genome Research
Living in a very specialized aquatic environment,
duckweeds do not need all essential genes of
terrestrial flowering plants, such as water transport, lignin biosynthesis, and cell wall-loosening
proteins. In fact, the Spirodela genome was
streamlined to be small (as the genome of Arabidopsis thaliana) with less than 20,000
protein-coding genes (three-quarters of A. thaliana genes). However, there are certain functional
categories of genes being enriched (e.g., ammonia
assimilation, defense-related processes) or specific (e.g., underlining mechanisms for fast growth,
aquatic life style or highly neotenous morphology) to duckweed genomes (Wang et al. 2014;
Van Hoeck et al. 2015). In this sense, comparative
genome analysis among duckweed genomes,
ideally with representative species of all five
genera, will help advance our knowledge of
duckweed genome structure and evolution. So far,
in addition to published genomes of S. polyrhiza
and Lemna minor, there have been several
on-going sequencing projects working on Spirodela intermedia, Landoltia punctata, Lemna
gibba, and Wolffia australiana. With the advent of
fast and cost-effective next-generation sequencing
platforms together with recent and continued
advances in third generation of long, singlemolecule sequencing platforms, it is imaginable
that further development of multiple technologies for effectively constructing long-range,
chromosome-size scaffolds will enable the complete assemblies of all 37 duckweed species
ranging from 158 Mbp to almost 2 Gbp.
In addition to the goal of gapless,
chromosome-scale genome assemblies, future
advances in technology, and growing interest of
research community may overcome the remaining hurdles on comprehensive understanding
duckweed gene functions, networks, and metabolic pathways. Although in many cases function
and biochemical activity of gene products may
be inferable from the presence of the common
and conserved protein domains, precise biological role and detailed functional information of
180
G. T. H. Vu et al.
addition to its nutritional value and fast biomass
production, these plants can purify highly concentrated waste streams into safe drinking water.
Importantly, duckweed production can possibly
be scalable from households (e.g., 5 L tanks),
small garden or village ponds to severalhectare-sized wastewater lagoons. Provided that
duckweed is globally distributed, duckweedbased solutions can be available on all continents
but Antarctica (for review, see Cao et al. 2018).
Fascinatingly, duckweed was additionally described as one of the most attractive higher plants for
long-duration supporting human life in space
(Yuan and Xu 2017). However, the implementation of these multi-purpose plants has still been
underrated partly due to currently incomplete
knowledge on duckweed biology and agriculture.
The availability of high-quality duckweed
reference genome sequences has ushered in new
and detailed insights into the mechanisms
underpinning biological processes of these
aquatic, highly morphologically reduced plant
models. The first duckweed genome Spirodela
polyrhiza (aka., the Greater Duckweed), chosen
due to its basal phylogenetic position and
smallest genome size, was sequenced by an
international consortium led by scientists from
Rutgers University (Wang et al. 2014). This
high-quality reference genome was improved to
the chromosome-level assembly by using
multi-color fluorescence in situ hybridization
(Cao et al. 2016a), optical mapping (Michael
et al. 2017), and Oxford Nanopore Technology
sequencing of another ecotype (aka., clone 9509)
of the same species (Hoang et al. 2018). Since
publication in 2014, the Spirodela genome has
been cited more than 100 times on the Google
Scholar indexing platform (dated July 2019),
serving as a duckweed reference genome not
only for greatly facilitating duckweed genomic
investigation (e.g., MAD box genes by Gramzow
and Theissen 2015; pentatricopeptide-repeat
proteins by Wang et al. 2016) but also for comparative genome analysis of other monocot and
aquatic plants (e.g., seagrass for angiosperm
adaptation to the sea by Olsen et al. 2016).
18.2 Future Prospects in Duckweed
Genome Research
Living in a very specialized aquatic environment,
duckweeds do not need all essential genes of
terrestrial flowering plants, such as water transport, lignin biosynthesis, and cell wall-loosening
proteins. In fact, the Spirodela genome was
streamlined to be small (as the genome of Arabidopsis thaliana) with less than 20,000
protein-coding genes (three-quarters of A. thaliana genes). However, there are certain functional
categories of genes being enriched (e.g., ammonia
assimilation, defense-related processes) or specific (e.g., underlining mechanisms for fast growth,
aquatic life style or highly neotenous morphology) to duckweed genomes (Wang et al. 2014;
Van Hoeck et al. 2015). In this sense, comparative
genome analysis among duckweed genomes,
ideally with representative species of all five
genera, will help advance our knowledge of
duckweed genome structure and evolution. So far,
in addition to published genomes of S. polyrhiza
and Lemna minor, there have been several
on-going sequencing projects working on Spirodela intermedia, Landoltia punctata, Lemna
gibba, and Wolffia australiana. With the advent of
fast and cost-effective next-generation sequencing
platforms together with recent and continued
advances in third generation of long, singlemolecule sequencing platforms, it is imaginable
that further development of multiple technologies for effectively constructing long-range,
chromosome-size scaffolds will enable the complete assemblies of all 37 duckweed species
ranging from 158 Mbp to almost 2 Gbp.
In addition to the goal of gapless,
chromosome-scale genome assemblies, future
advances in technology, and growing interest of
research community may overcome the remaining hurdles on comprehensive understanding
duckweed gene functions, networks, and metabolic pathways. Although in many cases function
and biochemical activity of gene products may
be inferable from the presence of the common
and conserved protein domains, precise biological role and detailed functional information of
180
G. T. H. Vu et al.