transposable elements account for 63% of the
Zostera assembly and tend to accumulate in
stretches of repeat elements which separating
gene-dense islands. Those observations indicate
typical genome shrinkage in S. polyrhiza by
eliminating non-essential protein-coding genes as
well as repetitive sequences (e.g. LTRs and
ribosomal DNA) probably due to deletiontowards-biases in DNA repair mechanisms
(Schubert and Vu 2016).
Duckweeds mainly proliferate by vegetative
budding of new fronds from the meristematic
zones, in a macroscopic manner analogous to
asexual propagation in yeast. With such clonal
propagation, duckweeds rapidly achieve massive
population sizes in nature as several millions of
individuals (i.e. ramets) can be found in a single
pond. In ecological aspect, using this reproductive
strategy, duckweeds have apparently well adapted
to large fluctuations that may rapidly occur in
aquatic habitats. The recurrent rejuvenation of
duckweed populations enhances the phenotypical
plasticity, allowing duckweeds to respond more
flexibly towards their changing environment.
Asexuality (i.e. lack of efficient recombination,
independent reassortment and segregation) is supposed to allow faster accumulation of chromosomal
mutations than in sexual or more frequently sexual
species (commonly known as the Meselson effect,
Weir et al. 2016). It could be a possible explanation
for controversial observations (UrbanskaWorytkiewicz 1980) of complex cytological
variations of duckweeds at multiple levels (i.e.
intra-individual, intra-population and interpopulation variations with aneuploid, mixoploid
and (endo)polyploids). However, how and to what
extent this reproductive strategy can have differential consequences on the plasticity and evolution
of duckweed genomes remain an open question and
a challenge for future work. Recent population
genomics investigations on geographically widespread clones of S. polyrhiza revealed a very low
genetic diversity which is likely due to a very low
mutation rate (i.e. one to two orders of magnitude
lower than Arabidopsis, Xu et al. 2019; Ho et al.
2019). Interestingly, diversity at nonsynonymous
sites relative to synonymous sites is shown to be
high, possibly suggesting a relaxed selection on
many genes due to the simplified form and lifestyle
of duckweeds. As more duckweed genomes are
reported from several ongoing whole-genome
sequencing projects of duckweeds, including
Spirodela intermedia, La. punctata, L. minor, L.
gibba and Wolffia australiana, these will pave the
way for the detailed understanding of such exciting
genome features, organization and genome
adaptation.
4.4 Epigenetic and Epigenomic
Aspects
Genomic DNA in eukaryotic cells is condensed
and packaged with histones to form a
DNA-protein complex known as chromatin at
various levels of folded structures. In interphase
nuclei, chromatin structures exhibit spatiotemporal dynamics both in the context of their
local condensation and nuclear positioning, presenting as the highly compact heterochromatin
and the less condensed euchromatin patterns.
Chromatin modifications (such as histone modifications and DNA methylation) are epigenetic
marks that had the potential to modify the degree
of chromatin condensation, and thus are the key
determinants of gene activities, cell fate and
genome stability. The advent of high-throughput
methods for genome-wide profiling of epigenetic
marks such as bisulphite sequencing (BSseq)
for DNA methylation and chromatin immunoprecipitation DNA-sequencing (ChIPseq) for
histone modifications has sparked interest in
studying the epigenetic modifications of chromatin in duckweeds, which to date has received
surprisingly little attention.
In conventional cytogenetic approaches,
chromatin staining, for example, with DNA
fluorochromes helps to visualize heterochromatin
and euchromatin as strongly stained and weakly
stained regions, respectively, under the microscope. The former usually corresponds to transcriptionally inactive, repetitive or gene-poor
genome regions, whereas the later corresponds to
transcriptionally active parts of the genome.
Günter Geber, in his thesis (1989), could recognize heterogeneity in duckweed nuclei by
54
X. H. Cao and G. T. H. Vu
Zostera assembly and tend to accumulate in
stretches of repeat elements which separating
gene-dense islands. Those observations indicate
typical genome shrinkage in S. polyrhiza by
eliminating non-essential protein-coding genes as
well as repetitive sequences (e.g. LTRs and
ribosomal DNA) probably due to deletiontowards-biases in DNA repair mechanisms
(Schubert and Vu 2016).
Duckweeds mainly proliferate by vegetative
budding of new fronds from the meristematic
zones, in a macroscopic manner analogous to
asexual propagation in yeast. With such clonal
propagation, duckweeds rapidly achieve massive
population sizes in nature as several millions of
individuals (i.e. ramets) can be found in a single
pond. In ecological aspect, using this reproductive
strategy, duckweeds have apparently well adapted
to large fluctuations that may rapidly occur in
aquatic habitats. The recurrent rejuvenation of
duckweed populations enhances the phenotypical
plasticity, allowing duckweeds to respond more
flexibly towards their changing environment.
Asexuality (i.e. lack of efficient recombination,
independent reassortment and segregation) is supposed to allow faster accumulation of chromosomal
mutations than in sexual or more frequently sexual
species (commonly known as the Meselson effect,
Weir et al. 2016). It could be a possible explanation
for controversial observations (UrbanskaWorytkiewicz 1980) of complex cytological
variations of duckweeds at multiple levels (i.e.
intra-individual, intra-population and interpopulation variations with aneuploid, mixoploid
and (endo)polyploids). However, how and to what
extent this reproductive strategy can have differential consequences on the plasticity and evolution
of duckweed genomes remain an open question and
a challenge for future work. Recent population
genomics investigations on geographically widespread clones of S. polyrhiza revealed a very low
genetic diversity which is likely due to a very low
mutation rate (i.e. one to two orders of magnitude
lower than Arabidopsis, Xu et al. 2019; Ho et al.
2019). Interestingly, diversity at nonsynonymous
sites relative to synonymous sites is shown to be
high, possibly suggesting a relaxed selection on
many genes due to the simplified form and lifestyle
of duckweeds. As more duckweed genomes are
reported from several ongoing whole-genome
sequencing projects of duckweeds, including
Spirodela intermedia, La. punctata, L. minor, L.
gibba and Wolffia australiana, these will pave the
way for the detailed understanding of such exciting
genome features, organization and genome
adaptation.
4.4 Epigenetic and Epigenomic
Aspects
Genomic DNA in eukaryotic cells is condensed
and packaged with histones to form a
DNA-protein complex known as chromatin at
various levels of folded structures. In interphase
nuclei, chromatin structures exhibit spatiotemporal dynamics both in the context of their
local condensation and nuclear positioning, presenting as the highly compact heterochromatin
and the less condensed euchromatin patterns.
Chromatin modifications (such as histone modifications and DNA methylation) are epigenetic
marks that had the potential to modify the degree
of chromatin condensation, and thus are the key
determinants of gene activities, cell fate and
genome stability. The advent of high-throughput
methods for genome-wide profiling of epigenetic
marks such as bisulphite sequencing (BSseq)
for DNA methylation and chromatin immunoprecipitation DNA-sequencing (ChIPseq) for
histone modifications has sparked interest in
studying the epigenetic modifications of chromatin in duckweeds, which to date has received
surprisingly little attention.
In conventional cytogenetic approaches,
chromatin staining, for example, with DNA
fluorochromes helps to visualize heterochromatin
and euchromatin as strongly stained and weakly
stained regions, respectively, under the microscope. The former usually corresponds to transcriptionally inactive, repetitive or gene-poor
genome regions, whereas the later corresponds to
transcriptionally active parts of the genome.
Günter Geber, in his thesis (1989), could recognize heterogeneity in duckweed nuclei by
54
X. H. Cao and G. T. H. Vu