genes. RNA 19:740–751. https://doi.org/10.
1261/rna.035279.112
55. Langmead B, Trapnell C, Pop M, Salzberg SL
(2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human
genome. Genome Biol 10:R25. https://doi.
org/10.1186/gb-2009-10-3-r25
56. Li H, Handsaker B, Wysoker A et al (2009)
The Sequence Alignment/Map format and
SAMtools. Bioinformatics 25:2078–2079.
https://doi.org/10.1093/bioinformatics/
btp352
57. Buels R, Yao E, Diesh CM et al (2016)
JBrowse: a dynamic web platform for genome
visualization and analysis. Genome Biol 17:66.
https://doi.org/10.1186/s13059-016-09241
58. Thorvaldsdottir H, Robinson JT, Mesirov JP
(2013) Integrative Genomics Viewer (IGV):
high-performance genomics data visualization
and exploration. Brief Bioinform 14:178–192.
https://doi.org/10.1093/bib/bbs017
59. Robinson JT, Thorvaldsdo ´ttir H, Winckler W
et al (2011) Integrative genomics viewer. Nat
Biotechnol 29:24–26. https://doi.org/10.
1038/nbt.1754
60. Brkljacic J, Grotewold E, Scholl R et al (2011)
Brachypodium as a model for the grasses: today
and the future. Plant Physiol 157:3–13.
https://doi.org/10.1104/pp.111.179531
61. Hirochika H, Okamoto H, Kakutani T (2000)
Silencing of retrotransposons in Arabidopsis
and reactivation by the ddm1 mutation. Plant
Cell 12:357–369. https://doi.org/10.1105/
tpc.12.3.357
62. Tsukahara S, Kobayashi A, Kawabe A et al
(2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461:423–426.
https://doi.org/10.1038/nature08351
63. Thieme M, Lanciano S, Balzergue S et al
(2017) Inhibition of RNA polymerase II allows
controlled mobilisation of retrotransposons for
plant breeding. Genome Biol 18:134. https://
doi.org/10.1186/s13059-017-1265-4
64. Akbergenov R, Si-Ammour A, Blevins T et al
(2006)
Molecular
characterization
of
geminivirus-derived small RNAs in different
plant species. Nucleic Acids Res 34:462–471.
https://doi.org/10.1093/nar/gkj447
65. Blevins T (2017) Northern blotting techniques
for small RNAs. Methods Mol Biol
1456:141–162.
https://doi.org/10.1007/
978-1-4899-7708-3_12
Genome-Scale and Northern Blot Analyses of siRNAs
411
1261/rna.035279.112
55. Langmead B, Trapnell C, Pop M, Salzberg SL
(2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human
genome. Genome Biol 10:R25. https://doi.
org/10.1186/gb-2009-10-3-r25
56. Li H, Handsaker B, Wysoker A et al (2009)
The Sequence Alignment/Map format and
SAMtools. Bioinformatics 25:2078–2079.
https://doi.org/10.1093/bioinformatics/
btp352
57. Buels R, Yao E, Diesh CM et al (2016)
JBrowse: a dynamic web platform for genome
visualization and analysis. Genome Biol 17:66.
https://doi.org/10.1186/s13059-016-09241
58. Thorvaldsdottir H, Robinson JT, Mesirov JP
(2013) Integrative Genomics Viewer (IGV):
high-performance genomics data visualization
and exploration. Brief Bioinform 14:178–192.
https://doi.org/10.1093/bib/bbs017
59. Robinson JT, Thorvaldsdo ´ttir H, Winckler W
et al (2011) Integrative genomics viewer. Nat
Biotechnol 29:24–26. https://doi.org/10.
1038/nbt.1754
60. Brkljacic J, Grotewold E, Scholl R et al (2011)
Brachypodium as a model for the grasses: today
and the future. Plant Physiol 157:3–13.
https://doi.org/10.1104/pp.111.179531
61. Hirochika H, Okamoto H, Kakutani T (2000)
Silencing of retrotransposons in Arabidopsis
and reactivation by the ddm1 mutation. Plant
Cell 12:357–369. https://doi.org/10.1105/
tpc.12.3.357
62. Tsukahara S, Kobayashi A, Kawabe A et al
(2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461:423–426.
https://doi.org/10.1038/nature08351
63. Thieme M, Lanciano S, Balzergue S et al
(2017) Inhibition of RNA polymerase II allows
controlled mobilisation of retrotransposons for
plant breeding. Genome Biol 18:134. https://
doi.org/10.1186/s13059-017-1265-4
64. Akbergenov R, Si-Ammour A, Blevins T et al
(2006)
Molecular
characterization
of
geminivirus-derived small RNAs in different
plant species. Nucleic Acids Res 34:462–471.
https://doi.org/10.1093/nar/gkj447
65. Blevins T (2017) Northern blotting techniques
for small RNAs. Methods Mol Biol
1456:141–162.
https://doi.org/10.1007/
978-1-4899-7708-3_12
Genome-Scale and Northern Blot Analyses of siRNAs
411