Duckweed (Spirodela polyrhiza, Michael et al.
2017; Wang et al. 2014) and one accession of the
Common Duckweed (Lemna minor, Van Hoeck
et al. 2015).
Spirodela genomes have a size of 158 Mbp
and organized into 20 chromosomes (2n = 40).
Interestingly, Spirodela has the fewest
protein-coding genes of sequenced angiosperms
at 18,507 for accession 9509 and at 19,623 for
accession 7498. With a three-fold larger genome
(481 Mbp) but also with 20 chromosome pairs,
Lemna minor accession 5500 contains a similar
number of protein-coding genes (18,744 high
confidence genes out of total 22,382 predicted
genes, Van Hoeck et al. 2015). These numbers
correspond to 30% less than that of Arabidopsis
thaliana and 50% less than that of monocotyledonous rice Oryza sativa. It is worthy to note that
Spirodela has undergone two successive rounds
(ca 95 Mya, likely coincident with the split
between duckweeds and the remaining monocot
family Araceae) of whole-genome duplications,
but yet has maintained a small genome size and a
small number of protein-coding genes. Comparing Spirodela predicted proteins with those of
plant reference genomes (e.g. A. thaliana, tomato
(Solanum lycopersicum), banana (Musa acuminata) and rice (Oryza sativa spp. indica)), there
are 1745 Spirodela-specific genes (8.9% of the
total predicted protein-coding genes), that are
enriched for various defence-related processes
(Wang et al. 2014). In addition, Spirodela gene
families showed a significantly reduced gene
number and preferential removal of duplicated
genes. Furthermore, the loss of several plant
conserved gene clusters, including genes
involved in water transport, biosynthesis of
phenylpropanoid and lignin as well as cell wall
organization is consistent with the miniature
plant body architecture and specialized ecological adaptation of Spirodela. However, in order to
optimize extremely fast growth, a few specific
gene families involved in ammonium assimilation and light harvesting are exceptionally
amplified. Lemna proteome is mostly (66%)
shared with the Spirodela proteome (Van Hoeck
et al. 2015), including a lineage-specific enrichment of proteins involved in adaptation to
various climate conditions, in removal of surplus
nutrients from wastewater, and in providing
nutritional value and high biomass productivity.
The increasing wealth of complete
whole-genome sequences highlights the critical
role of transposable elements (TEs) in plant
genome evolution. These mobile genetic elements function as a driver of drastic changes in
genome size and as an important source of new
variants in coding and regulatory sequences.
Transposable elements (TEs) constitute 16 to
25% of the Spirodela genomes 7498 and 9509,
respectively, while A. thaliana genomes has
roughly similar nuclear genome size (135–157
Mbp, Bennett et al. 2003) and similar TE content
(15–24%, The Arabidopsis Genome Initiative
2000; Hu et al. 2011). Given that repetitive
sequences comprise 62% of the L. minor genome
assembly, repeat content explains 94% of the
genome size difference between sequenced Spirodela and Lemna genomes (Van Hoeck et al.
2015). A detailed look on sequences of long terminal repeats (LTRs) in the Spirodela genomes
suggests that the intact LTRs are old (*4 Mya)
and a high proportion of LTRs contains one terminal repeat without its pair or internal sequence
(solo LTRs). Moreover, Spirodela genomes are
streamlined with less than 100 copies of ribosomal DNA, corresponding to 15% of that in Arabidopsis genome (Michael et al. 2017).
The whole-genome sequence of seagrass
Zostera marina or eelgrass (the only other
sequenced alismatid with the 202 Mb genome
and 20,450 protein-coding genes) which diverged
from the common ancestor (Alismatales, Araceae) with duckweeds between 135 and 107
million years ago (Olsen et al. 2016) provides
new insights on the alismatid lineage with the
stage for the terrestrial-freshwater and the subsequent freshwater-marine transitions. Since the
split from Z. marina, Spirodela has gained 292
protein domains (Pfam database), 40 of which
appear to be unique. Interestingly, 519 protein
domains have been lost, while 467 protein
domains have contracted in the Spirodela proteome. These numbers are more than twice of the
corresponding numbers of Z. marina (146 and
162 protein domains, respectively). In addition,
4 Cytogenetics, Epigenetics and Karyotype Evolution of Duckweeds
53
2017; Wang et al. 2014) and one accession of the
Common Duckweed (Lemna minor, Van Hoeck
et al. 2015).
Spirodela genomes have a size of 158 Mbp
and organized into 20 chromosomes (2n = 40).
Interestingly, Spirodela has the fewest
protein-coding genes of sequenced angiosperms
at 18,507 for accession 9509 and at 19,623 for
accession 7498. With a three-fold larger genome
(481 Mbp) but also with 20 chromosome pairs,
Lemna minor accession 5500 contains a similar
number of protein-coding genes (18,744 high
confidence genes out of total 22,382 predicted
genes, Van Hoeck et al. 2015). These numbers
correspond to 30% less than that of Arabidopsis
thaliana and 50% less than that of monocotyledonous rice Oryza sativa. It is worthy to note that
Spirodela has undergone two successive rounds
(ca 95 Mya, likely coincident with the split
between duckweeds and the remaining monocot
family Araceae) of whole-genome duplications,
but yet has maintained a small genome size and a
small number of protein-coding genes. Comparing Spirodela predicted proteins with those of
plant reference genomes (e.g. A. thaliana, tomato
(Solanum lycopersicum), banana (Musa acuminata) and rice (Oryza sativa spp. indica)), there
are 1745 Spirodela-specific genes (8.9% of the
total predicted protein-coding genes), that are
enriched for various defence-related processes
(Wang et al. 2014). In addition, Spirodela gene
families showed a significantly reduced gene
number and preferential removal of duplicated
genes. Furthermore, the loss of several plant
conserved gene clusters, including genes
involved in water transport, biosynthesis of
phenylpropanoid and lignin as well as cell wall
organization is consistent with the miniature
plant body architecture and specialized ecological adaptation of Spirodela. However, in order to
optimize extremely fast growth, a few specific
gene families involved in ammonium assimilation and light harvesting are exceptionally
amplified. Lemna proteome is mostly (66%)
shared with the Spirodela proteome (Van Hoeck
et al. 2015), including a lineage-specific enrichment of proteins involved in adaptation to
various climate conditions, in removal of surplus
nutrients from wastewater, and in providing
nutritional value and high biomass productivity.
The increasing wealth of complete
whole-genome sequences highlights the critical
role of transposable elements (TEs) in plant
genome evolution. These mobile genetic elements function as a driver of drastic changes in
genome size and as an important source of new
variants in coding and regulatory sequences.
Transposable elements (TEs) constitute 16 to
25% of the Spirodela genomes 7498 and 9509,
respectively, while A. thaliana genomes has
roughly similar nuclear genome size (135–157
Mbp, Bennett et al. 2003) and similar TE content
(15–24%, The Arabidopsis Genome Initiative
2000; Hu et al. 2011). Given that repetitive
sequences comprise 62% of the L. minor genome
assembly, repeat content explains 94% of the
genome size difference between sequenced Spirodela and Lemna genomes (Van Hoeck et al.
2015). A detailed look on sequences of long terminal repeats (LTRs) in the Spirodela genomes
suggests that the intact LTRs are old (*4 Mya)
and a high proportion of LTRs contains one terminal repeat without its pair or internal sequence
(solo LTRs). Moreover, Spirodela genomes are
streamlined with less than 100 copies of ribosomal DNA, corresponding to 15% of that in Arabidopsis genome (Michael et al. 2017).
The whole-genome sequence of seagrass
Zostera marina or eelgrass (the only other
sequenced alismatid with the 202 Mb genome
and 20,450 protein-coding genes) which diverged
from the common ancestor (Alismatales, Araceae) with duckweeds between 135 and 107
million years ago (Olsen et al. 2016) provides
new insights on the alismatid lineage with the
stage for the terrestrial-freshwater and the subsequent freshwater-marine transitions. Since the
split from Z. marina, Spirodela has gained 292
protein domains (Pfam database), 40 of which
appear to be unique. Interestingly, 519 protein
domains have been lost, while 467 protein
domains have contracted in the Spirodela proteome. These numbers are more than twice of the
corresponding numbers of Z. marina (146 and
162 protein domains, respectively). In addition,
4 Cytogenetics, Epigenetics and Karyotype Evolution of Duckweeds
53