LT5a, and 1% in 7498. In other plant species,
24nt RNAs are a part of the RNA-directed DNA
methylation pathway where transposons are
transcribed into single-stranded and then
double-stranded RNA, diced into 24nt heterochromatic small RNAs, and then used to guide
a protein network that methylates matching
sequences and then silences them as heterochromatin. Accordingly, Michael et al. also
studied DNA methylation in the Spirodela 9509
genome and found it to be the least methylated
plant sequenced! This DNA methylation pathway in duckweeds is a new and exciting field of
study summarized in Chap. 5 that appears to be
the cutting edge of small RNA research in the
Lemnaceae.
Acknowledgements I would like to thank Professor Jie
Tang of Chengdu University for providing data on his
submitted and published work respectively and reviewing
this manuscript to ensure its accuracy.
References
Afgan E, Baker D, van den Beek M et al (2016) The
galaxy platform for accessible, reproducible and
collaborative biomedical analyses: 2016 update.
Nucleic Acids Res 44:W3–W10. https://doi.org/10.
1093/nar/gkw343
An J, Lai J, Sajjanhar A et al (2014) miRPlant: an
integrated tool for identification of plant miRNA from
RNA sequencing data. BMC Bioinform 15:275.
https://doi.org/10.1186/1471-2105-15-275
Axtell MJ, Meyers BC (2018) Revisiting criteria for plant
miRNA annotation in the era of big data. Plant Cell
30:tpc.00851.2017.
https://doi.org/10.1105/tpc.17.
00851
Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990)
The product of the H19 gene may function as an RNA.
Mol Cell Biol 10:28–36. https://doi.org/10.1128/
MCB.10.1.28
Dai X, Zhao PX (2011) PsRNATarget: A plant small
RNA target analysis server. Nucleic Acids Res 39:
W155–W159. https://doi.org/10.1093/nar/gkr319
Denman RB (1993) Using RNAFOLD to predict the
activity of small catalytic RNAs. Biotechniques
15:1090–1095
Fahlgren N, Carrington JC (2010) miRNA target prediction in plants. Humana Press, pp 51–57
Franco-Zorrilla JM, Valli A, Todesco M et al (2007)
Target mimicry provides a new mechanism for
regulation of microRNA activity. Nat Genet 398
(39):1033. https://doi.org/10.1038/ng2079
Griffiths-Jones SM (2006) The microRNA sequence
database. Methods Mol Biol 342:129–138
Howell MD, Fahlgren N, Chapman EJ et al (2007)
Genome-wide analysis of the RNA-dependent RNA
POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and
tasiRNA-directed targeting. Plant Cell 19:926–942.
https://doi.org/10.1105/tpc.107.050062
Johnson C, Kasprzewska A, Tennessen K et al (2009)
Clusters and superclusters of phased small RNAs in
the developing inflorescence of rice. Genome Res
19:1429–1440. https://doi.org/10.1101/gr.089854.108
Jones-Rhoades MW, Bartel DP (2004) Computational
identification of plant MicroRNAs and their targets,
including a stress-induced miRNA. Mol Cell 14:787–
799. https://doi.org/10.1016/J.MOLCEL.2004.05.027
Kakrana A, Hammond R, Patel P et al (2014) SPARTA: a
parallelized pipeline for integrated analysis of plant
miRNA and cleaved mRNA data sets, including new
miRNA target-identification software. Nucleic Acids
Res 42:1–13. https://doi.org/10.1093/nar/gku693
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
Li Y-F, Zheng Y, Addo-Quaye C et al (2010)
Transcriptome-wide identification of microRNA targets in rice. Plant J 62:742–759. https://doi.org/10.
1111/j.1365-313X.2010.04187.x
Meyers BC, Axtell MJ, Bartel B et al (2008) Criteria for
annotation of plant MicroRNAs. Plant Cell 20:3186–
3190. https://doi.org/10.1105/tpc.108.064311
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
Nakano M, Nobuta K, Vemaraju K et al (2006)
Plant MPSS databases: signature-based transcriptional
resources for analyses of mRNA and small RNA.
Nucleic Acids Res 34:D731–D735. https://doi.org/10.
1093/nar/gkj077
Scott MS, Ono M (2011) From snoRNA to miRNA: dual
function regulatory non-coding RNAs. Biochimie
93:1987–1992.
https://doi.org/10.1016/J.BIOCHI.
2011.05.026
Song C, Wang C, Zhang C et al (2010) Deep sequencing
discovery of novel and conserved microRNAs in
trifoliate orange (citrus trifoliata). BMC Genom
11:431. https://doi.org/10.1186/1471-2164-11-431
Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ (2014)
Evolutionary history of plant microRNAs. Trends
Plant Sci 19:175–182. https://doi.org/10.1016/J.
TPLANTS.2013.11.008
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
5:1–13. https://doi.org/10.1038/ncomms4311
16 Small RNAs in Duckweeds
163
24nt RNAs are a part of the RNA-directed DNA
methylation pathway where transposons are
transcribed into single-stranded and then
double-stranded RNA, diced into 24nt heterochromatic small RNAs, and then used to guide
a protein network that methylates matching
sequences and then silences them as heterochromatin. Accordingly, Michael et al. also
studied DNA methylation in the Spirodela 9509
genome and found it to be the least methylated
plant sequenced! This DNA methylation pathway in duckweeds is a new and exciting field of
study summarized in Chap. 5 that appears to be
the cutting edge of small RNA research in the
Lemnaceae.
Acknowledgements I would like to thank Professor Jie
Tang of Chengdu University for providing data on his
submitted and published work respectively and reviewing
this manuscript to ensure its accuracy.
References
Afgan E, Baker D, van den Beek M et al (2016) The
galaxy platform for accessible, reproducible and
collaborative biomedical analyses: 2016 update.
Nucleic Acids Res 44:W3–W10. https://doi.org/10.
1093/nar/gkw343
An J, Lai J, Sajjanhar A et al (2014) miRPlant: an
integrated tool for identification of plant miRNA from
RNA sequencing data. BMC Bioinform 15:275.
https://doi.org/10.1186/1471-2105-15-275
Axtell MJ, Meyers BC (2018) Revisiting criteria for plant
miRNA annotation in the era of big data. Plant Cell
30:tpc.00851.2017.
https://doi.org/10.1105/tpc.17.
00851
Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990)
The product of the H19 gene may function as an RNA.
Mol Cell Biol 10:28–36. https://doi.org/10.1128/
MCB.10.1.28
Dai X, Zhao PX (2011) PsRNATarget: A plant small
RNA target analysis server. Nucleic Acids Res 39:
W155–W159. https://doi.org/10.1093/nar/gkr319
Denman RB (1993) Using RNAFOLD to predict the
activity of small catalytic RNAs. Biotechniques
15:1090–1095
Fahlgren N, Carrington JC (2010) miRNA target prediction in plants. Humana Press, pp 51–57
Franco-Zorrilla JM, Valli A, Todesco M et al (2007)
Target mimicry provides a new mechanism for
regulation of microRNA activity. Nat Genet 398
(39):1033. https://doi.org/10.1038/ng2079
Griffiths-Jones SM (2006) The microRNA sequence
database. Methods Mol Biol 342:129–138
Howell MD, Fahlgren N, Chapman EJ et al (2007)
Genome-wide analysis of the RNA-dependent RNA
POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and
tasiRNA-directed targeting. Plant Cell 19:926–942.
https://doi.org/10.1105/tpc.107.050062
Johnson C, Kasprzewska A, Tennessen K et al (2009)
Clusters and superclusters of phased small RNAs in
the developing inflorescence of rice. Genome Res
19:1429–1440. https://doi.org/10.1101/gr.089854.108
Jones-Rhoades MW, Bartel DP (2004) Computational
identification of plant MicroRNAs and their targets,
including a stress-induced miRNA. Mol Cell 14:787–
799. https://doi.org/10.1016/J.MOLCEL.2004.05.027
Kakrana A, Hammond R, Patel P et al (2014) SPARTA: a
parallelized pipeline for integrated analysis of plant
miRNA and cleaved mRNA data sets, including new
miRNA target-identification software. Nucleic Acids
Res 42:1–13. https://doi.org/10.1093/nar/gku693
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
Li Y-F, Zheng Y, Addo-Quaye C et al (2010)
Transcriptome-wide identification of microRNA targets in rice. Plant J 62:742–759. https://doi.org/10.
1111/j.1365-313X.2010.04187.x
Meyers BC, Axtell MJ, Bartel B et al (2008) Criteria for
annotation of plant MicroRNAs. Plant Cell 20:3186–
3190. https://doi.org/10.1105/tpc.108.064311
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
Nakano M, Nobuta K, Vemaraju K et al (2006)
Plant MPSS databases: signature-based transcriptional
resources for analyses of mRNA and small RNA.
Nucleic Acids Res 34:D731–D735. https://doi.org/10.
1093/nar/gkj077
Scott MS, Ono M (2011) From snoRNA to miRNA: dual
function regulatory non-coding RNAs. Biochimie
93:1987–1992.
https://doi.org/10.1016/J.BIOCHI.
2011.05.026
Song C, Wang C, Zhang C et al (2010) Deep sequencing
discovery of novel and conserved microRNAs in
trifoliate orange (citrus trifoliata). BMC Genom
11:431. https://doi.org/10.1186/1471-2164-11-431
Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ (2014)
Evolutionary history of plant microRNAs. Trends
Plant Sci 19:175–182. https://doi.org/10.1016/J.
TPLANTS.2013.11.008
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
5:1–13. https://doi.org/10.1038/ncomms4311
16 Small RNAs in Duckweeds
163