modeling and DNA methylation studies (Cao
et al. 2016; Michael et al. 2017), and in a
physiological sense where the studies of turion
development, for example, can be linked to the
results (Kuehdorf et al. 2014). As it stands the
research community can observe the Spirodela
transcriptome in two or eight conditions as
mRNA expression, editing, and degradation. It is
expected that the transcriptional research will
expand to include more stimuli exposure, tissue
specific, life cycle, and microbe interaction
experiments. These Spirodela genomes and
transcriptome studies facilitate research across
the family by providing a reference for the other
genomes or transcriptomes. Even in cases of de
novo assemblies and isoform sequencing of any
other related species the Spirodela genome will
provide annotated and characterized gene
models.
References
An D, Cao H, Li C et al (2018a) Isoform sequencing and
state-of-art applications for unravelling complexity of
plant transcriptomes. Genes (Basel) 9:43. https://doi.
org/10.3390/genes9010043
An D, Li C, Zhou Y et al (2018b) Genomes and
transcriptomes of duckweeds. Front Chem 6. https://
doi.org/10.3389/fchem.2018.00230
Barkan A, Rojas M, Fujii S et al (2012) A combinatorial
amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 8:e1002910.
https://doi.org/10.1371/journal.pgen.1002910
Cao HX, Vu GTH, Wang W et al (2016) The map-based
genome sequence of Spirodela polyrhiza aligned with
its chromosomes, a reference for karyotype evolution.
New Phytol 209:354–363. https://doi.org/10.1111/
nph.13592
Cieślik M, Chinnaiyan AM (2017) Cancer transcriptome
profiling at the juncture of clinical translation. Nat Rev
Genet 19:93–109. https://doi.org/10.1038/nrg.2017.96
Fourounjian P, Tang J, Tanyolac B, Feng Y, Gelfand B,
Kakrana A, Tu M, Wakim C, Meyers BC, Ma J,
Messing J (2019) Post‐transcriptional adaptation of the
aquatic plant under stress and hormonal stimuli. Plant J
Kuehdorf K, Jetschke G, Ballani L, Appenroth K-J (2014)
The clonal dependence of turion formation in the
duckweed Spirodela polyrhiza—an ecogeographical
approach. Physiol Plant 150:46–54. https://doi.org/10.
1111/ppl.12065
Manna S (2015) An overview of pentatricopeptide repeat
proteins and their applications. Biochimie 113:93–99.
https://doi.org/10.1016/J.BIOCHI.2015.04.004
Michael TP, Bryant D, Gutierrez R et al (2017) Comprehensive definition of genome features in Spirodela
polyrhiza by high-depth physical mapping and
short-read DNA sequencing strategies. Plant J
89:617–635. https://doi.org/10.1111/tpj.13400
Tao X, Fang Y, Xiao Y et al (2013) Comparative
transcriptome analysis to investigate the high starch
accumulation of duckweed (Landoltia punctata) under
nutrient starvation. Biotechnol Biofuels 6:72. https://
doi.org/10.1186/1754-6834-6-72
Van Hoeck A, Horemans N, Monsieurs P et al (2015) The
first draft genome of the aquatic model plant Lemna
minor opens the route for future stress physiology
research and biotechnological applications. Biotechnol
Biofuels 8:1–13. https://doi.org/10.1186/s13068-0150381-1
Wang W, Haberer G, Gundlach H et al (2014a) The
Spirodela polyrhiza genome reveals insights into its
neotenous reduction fast growth and aquatic lifestyle.
Nat Commun 5. https://doi.org/10.1038/ncomms4311
Wang W, Wu Y, Messing J (2014b) RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction. BMC Genom 15:60. https://doi.org/10.1186/
1471-2164-15-60
Wang W, Zhang W, Wu Y et al (2015) RNA editing in
chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species. PLoS ONE 10:e0140285.
https://doi.org/10.1371/journal.pone.0140285
Wang W, Li R, Zhu Q et al (2016) Transcriptomic and
physiological analysis of common duckweed Lemna
minor responses to NH4+ toxicity. BMC Plant Biol
16:92. https://doi.org/10.1186/s12870-016-0774-8
Yu C, Zhao X, Qi G et al (2017) Integrated analysis of
transcriptome and metabolites reveals an essential role
of metabolic flux in starch accumulation under
nitrogen starvation in duckweed. Biotechnol Biofuels
10:167. https://doi.org/10.1186/s13068-017-0851-8
136
P. Fourounjian
et al. 2016; Michael et al. 2017), and in a
physiological sense where the studies of turion
development, for example, can be linked to the
results (Kuehdorf et al. 2014). As it stands the
research community can observe the Spirodela
transcriptome in two or eight conditions as
mRNA expression, editing, and degradation. It is
expected that the transcriptional research will
expand to include more stimuli exposure, tissue
specific, life cycle, and microbe interaction
experiments. These Spirodela genomes and
transcriptome studies facilitate research across
the family by providing a reference for the other
genomes or transcriptomes. Even in cases of de
novo assemblies and isoform sequencing of any
other related species the Spirodela genome will
provide annotated and characterized gene
models.
References
An D, Cao H, Li C et al (2018a) Isoform sequencing and
state-of-art applications for unravelling complexity of
plant transcriptomes. Genes (Basel) 9:43. https://doi.
org/10.3390/genes9010043
An D, Li C, Zhou Y et al (2018b) Genomes and
transcriptomes of duckweeds. Front Chem 6. https://
doi.org/10.3389/fchem.2018.00230
Barkan A, Rojas M, Fujii S et al (2012) A combinatorial
amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 8:e1002910.
https://doi.org/10.1371/journal.pgen.1002910
Cao HX, Vu GTH, Wang W et al (2016) The map-based
genome sequence of Spirodela polyrhiza aligned with
its chromosomes, a reference for karyotype evolution.
New Phytol 209:354–363. https://doi.org/10.1111/
nph.13592
Cieślik M, Chinnaiyan AM (2017) Cancer transcriptome
profiling at the juncture of clinical translation. Nat Rev
Genet 19:93–109. https://doi.org/10.1038/nrg.2017.96
Fourounjian P, Tang J, Tanyolac B, Feng Y, Gelfand B,
Kakrana A, Tu M, Wakim C, Meyers BC, Ma J,
Messing J (2019) Post‐transcriptional adaptation of the
aquatic plant under stress and hormonal stimuli. Plant J
Kuehdorf K, Jetschke G, Ballani L, Appenroth K-J (2014)
The clonal dependence of turion formation in the
duckweed Spirodela polyrhiza—an ecogeographical
approach. Physiol Plant 150:46–54. https://doi.org/10.
1111/ppl.12065
Manna S (2015) An overview of pentatricopeptide repeat
proteins and their applications. Biochimie 113:93–99.
https://doi.org/10.1016/J.BIOCHI.2015.04.004
Michael TP, Bryant D, Gutierrez R et al (2017) Comprehensive definition of genome features in Spirodela
polyrhiza by high-depth physical mapping and
short-read DNA sequencing strategies. Plant J
89:617–635. https://doi.org/10.1111/tpj.13400
Tao X, Fang Y, Xiao Y et al (2013) Comparative
transcriptome analysis to investigate the high starch
accumulation of duckweed (Landoltia punctata) under
nutrient starvation. Biotechnol Biofuels 6:72. https://
doi.org/10.1186/1754-6834-6-72
Van Hoeck A, Horemans N, Monsieurs P et al (2015) The
first draft genome of the aquatic model plant Lemna
minor opens the route for future stress physiology
research and biotechnological applications. Biotechnol
Biofuels 8:1–13. https://doi.org/10.1186/s13068-0150381-1
Wang W, Haberer G, Gundlach H et al (2014a) The
Spirodela polyrhiza genome reveals insights into its
neotenous reduction fast growth and aquatic lifestyle.
Nat Commun 5. https://doi.org/10.1038/ncomms4311
Wang W, Wu Y, Messing J (2014b) RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction. BMC Genom 15:60. https://doi.org/10.1186/
1471-2164-15-60
Wang W, Zhang W, Wu Y et al (2015) RNA editing in
chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species. PLoS ONE 10:e0140285.
https://doi.org/10.1371/journal.pone.0140285
Wang W, Li R, Zhu Q et al (2016) Transcriptomic and
physiological analysis of common duckweed Lemna
minor responses to NH4+ toxicity. BMC Plant Biol
16:92. https://doi.org/10.1186/s12870-016-0774-8
Yu C, Zhao X, Qi G et al (2017) Integrated analysis of
transcriptome and metabolites reveals an essential role
of metabolic flux in starch accumulation under
nitrogen starvation in duckweed. Biotechnol Biofuels
10:167. https://doi.org/10.1186/s13068-017-0851-8
136
P. Fourounjian