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008
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org/10.1038/s41598-017-06174-3
48. Goodstein DM, Shu S, Howson R et al (2012)
Phytozome: a comparative platform for green
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nar/gkr944
49. International Brachypodium Initiative (2010)
Genome sequencing and analysis of the model
grass Brachypodium distachyon. Nature
463:763–768.
https://doi.org/10.1038/
nature08747
50. Jeong D-H, Schmidt SA, Rymarquis LA et al
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global investigation of microRNAs and target
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Biol 14:R145. https://doi.org/10.1186/gb2013-14-12-r145
51. Gremme G, Steinbiss S, Kurtz S (2013) GenomeTools: a comprehensive software library for
efficient processing of structured genome
annotations. IEEE/ACM Trans Comput Biol
Bioinform 10:645–656. https://doi.org/10.
1109/TCBB.2013.68
52. Martin M (2011) Cutadapt removes adapter
sequences from high-throughput sequencing
reads. EMBnet J 17:10. https://doi.org/10.
14806/ej.17.1.200
53. Johnson NR, Yeoh JM, Coruh C, Axtell MJ
(2016) Improved placement of multi-mapping
small RNAs. G3 (Bethesda) 6:2103–2111.
https://doi.org/10.1534/G3.116.030452
54. Axtell MJ (2013) ShortStack: comprehensive
annotation and quantification of small RNA
410
Marcel Bo ¨ hrer et al.
41:630–634. https://doi.org/10.1038/ng.
365
32. Blevins T, Pontvianne F, Cocklin R et al (2014)
A two-step process for epigenetic inheritance in
Arabidopsis. Mol Cell 54:30–42. https://doi.
org/10.1016/j.molcel.2014.02.019
33. Ito H, Gaubert H, Bucher E et al (2011) An
siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress.
Nature 472:115–119. https://doi.org/10.
1038/nature09861
34. Mirouze M, Reinders J, Bucher E et al (2009)
Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461:427–430.
https://doi.org/10.1038/nature08328
35. Lanciano S, Mirouze M (2018) Transposable
elements: all mobile, all different, some stress
responsive, some adaptive? Curr Opin Genet
Dev 49:106–114. https://doi.org/10.1016/
j.gde.2018.04.002
36. Grandbastien M-A (2015) LTR retrotransposons, handy hitchhikers of plant regulation and
stress response. Biochim Biophys Acta
1849:403–416. https://doi.org/10.1016/j.
bbagrm.2014.07.017
37. Cavrak VV, Lettner N, Jamge S et al (2014)
How a retrotransposon exploits the plant’s heat
stress response for its activation. PLoS Genet
10:e1004115. https://doi.org/10.1371/jour
nal.pgen.1004115
38. Pietzenuk B, Markus C, Gaubert H et al
(2016) Recurrent evolution of heatresponsiveness in Brassicaceae COPIA elements. Genome Biol 17:209. https://doi.
org/10.1186/s13059-016-1072-3
39. Platt RN 2nd, Blanco-Berdugo L, Ray DA
(2016) Accurate transposable element annotation is vital when analyzing new genome assemblies. Genome Biol Evol 8:403–410
40. Underwood CJ, Henderson IR, Martienssen
RA (2017) Genetic and epigenetic variation of
transposable elements in Arabidopsis. Curr
Opin Plant Biol 36:135–141. https://doi.
org/10.1016/J.PBI.2017.03.002
41. El Baidouri M, Do KK, Abernathy B et al
(2015) A new approach for annotation of
transposable elements using small RNA
mapping. Nucleic Acids Res e84:43. https://
doi.org/10.1093/nar/gkv257
42. Ahmed I, Sarazin A, Bowler C et al (2011)
Genome-wide evidence for local DNA methylation spreading from small RNA-targeted
sequences in Arabidopsis. Nucleic Acids Res
39:6919–6931.
https://doi.org/10.1093/
nar/gkr324
43. Forestan C, Farinati S, Aiese Cigliano R et al
(2017) Maize RNA PolIV affects the expression of genes with nearby TE insertions and has
a genome-wide repressive impact on transcription. BMC Plant Biol 17:161. https://doi.
org/10.1186/s12870-017-1108-1
44. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of
the genome. Nat Rev Genet 8:272–285.
https://doi.org/10.1038/nrg2072
45. Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant
Biol 64:137–159. https://doi.org/10.1146/
annurev-arplant-050312-120043
46. Meyers BC, Souret FF, Lu C, Green PJ (2006)
Sweating the small stuff: microRNA discovery
in plants. Curr Opin Biotechnol 17:139–146.
https://doi.org/10.1016/j.copbio.2006.01.
008
47. Lutzmayer S, Enugutti B, Nodine MD (2017)
Novel small RNA spike-in oligonucleotides
enable absolute normalization of small
RNA-Seq data. Sci Rep 7:5913. https://doi.
org/10.1038/s41598-017-06174-3
48. Goodstein DM, Shu S, Howson R et al (2012)
Phytozome: a comparative platform for green
plant genomics. Nucleic Acids Res 40:
D1178–D1186. https://doi.org/10.1093/
nar/gkr944
49. International Brachypodium Initiative (2010)
Genome sequencing and analysis of the model
grass Brachypodium distachyon. Nature
463:763–768.
https://doi.org/10.1038/
nature08747
50. Jeong D-H, Schmidt SA, Rymarquis LA et al
(2013) Parallel analysis of RNA ends enhances
global investigation of microRNAs and target
RNAs of Brachypodium distachyon. Genome
Biol 14:R145. https://doi.org/10.1186/gb2013-14-12-r145
51. Gremme G, Steinbiss S, Kurtz S (2013) GenomeTools: a comprehensive software library for
efficient processing of structured genome
annotations. IEEE/ACM Trans Comput Biol
Bioinform 10:645–656. https://doi.org/10.
1109/TCBB.2013.68
52. Martin M (2011) Cutadapt removes adapter
sequences from high-throughput sequencing
reads. EMBnet J 17:10. https://doi.org/10.
14806/ej.17.1.200
53. Johnson NR, Yeoh JM, Coruh C, Axtell MJ
(2016) Improved placement of multi-mapping
small RNAs. G3 (Bethesda) 6:2103–2111.
https://doi.org/10.1534/G3.116.030452
54. Axtell MJ (2013) ShortStack: comprehensive
annotation and quantification of small RNA
410
Marcel Bo ¨ hrer et al.