40. Lin SY, Chen PW, Chuang MH, Juntawong P,
Bailey-Serres J, Jauh GY (2014) Profiling of
translatomes of in vivo-grown pollen tubes
reveals genes with roles in micropylar guidance
during pollination in Arabidopsis. Plant Cell
26:602–618
41. Tian C, Wang Y, Yu H, He J, Wang J, Shi B,
Du Q, Provart NJ, Meyerowitz EM, Jiao Y
(2019) A gene expression map of shoot
domains reveals regulatory mechanisms. Nat
Commun 10:141
42. Reynoso MA, Blanco FA, Bailey-Serres J,
Crespi M, Zanetti ME (2013) Selective recruitment of mRNAs and miRNAs to polyribosomes in response to rhizobia infection in
Medicago truncatula. Plant J 73:289–301
43. Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S,
Masson H, Inagaki S, Federici F, Sinha N,
Deal RB, Bailey-Serres J, Brady SM (2014)
Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell
type-specific gene expression and function
using tomato as a model. Plant Physiol
166:455–469
44. Zhao D, Hamilton JP, Hardigan M, Yin D,
He T, Vaillancourt B, Reynoso M,
Pauluzzi G, Funkhouser S, Cui Y, BaileySerres J, Jiang J, Buell CR, Jiang N (2017)
Analysis of ribosome-associated mRNAs in
rice reveals the importance of transcript size
and GC content in translation. G3 (Bethesda)
7:203–219
45. Castro-Guerrero NA, Cui Y, Mendoza-Cozatl
DG (2016) Purification of translating ribosomes and associated mRNAs from soybean
(Glycine max). Curr Protoc Plant Biol
1:185–196
46. Reynoso MA, Juntawong P, Lancia M, Blanco
FA, Bailey-Serres J, Zanetti ME (2015) Translating ribosome affinity purification (TRAP)
followed by RNA sequencing technology
(TRAP-SEQ) for quantitative assessment of
plant translatomes. Methods Mol Biol
1284:185–207
47. Reynoso MA, Pauluzzi GC, Kajala K,
Cabanlit S, Velasco J, Bazin J, Deal R, Sinha
NR, Brady SM, Bailey-Serres J (2018) Nuclear
transcriptomes at high resolution using
retooled INTACT. Plant Physiol 176:270–281
48. Townsley BT, Covington MF, Ichihashi Y,
Zumstein K, Sinha NR (2015) BrAD-seq:
breath adapter directional sequencing: a
streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA
library construction. Front Plant Sci 6:366
49. Blankenberg D, Gordon A, Von Kuster G,
Coraor N, Taylor J, Nekrutenko A (2010)
Manipulation of FASTQ data with Galaxy. Bioinformatics 26:1783–1785
50. Trapnell C, Pachter L, Salzberg SL (2009)
TopHat: discovering splice junctions with
RNA-Seq. Bioinformatics 25:1105–1111
51. Kim D, Langmead B, Salzberg SL (2015)
HISAT: a fast spliced aligner with low memory
requirements. Nat Methods 12:357
52. Trapnell C, Williams BA, Pertea G,
Mortazavi A, Kwan G, van Baren MJ, Salzberg
SL, Wold BJ, Pachter L (2010) Transcript
assembly and quantification by RNA-Seq
reveals unannotated transcripts and isoform
switching during cell differentiation. Nat Biotechnol 28:511
53. Thorvaldsdottir H, Robinson JT, Mesirov JP
(2013) Integrative genomics viewer (IGV):
high-performance genomics data visualization
and exploration. Brief Bioinform 14:178–192
54. Kang YJ, Yang DC, Kong L, Hou M, Meng
YQ, L W, Gao G (2017) CPC2: a fast and
accurate coding potential calculator based on
sequence intrinsic features. Nucleic Acids Res
45:W12–W16
55. Wang L, Park HJ, Dasari S, Wang S, Kocher JP,
Li W (2013) CPAT: coding-potential assessment tool using an alignment-free logistic
regression model. Nucleic Acids Res 41:e74
56. Hezroni H, Koppstein D, Schwartz MG,
Avrutin A, Bartel DP, Ulitsky I (2015) Principles of long noncoding RNA evolution derived
from direct comparison of transcriptomes in
17 species. Cell Rep 11:1110–1122
472
Soledad Traubenik et al.
Bailey-Serres J, Jauh GY (2014) Profiling of
translatomes of in vivo-grown pollen tubes
reveals genes with roles in micropylar guidance
during pollination in Arabidopsis. Plant Cell
26:602–618
41. Tian C, Wang Y, Yu H, He J, Wang J, Shi B,
Du Q, Provart NJ, Meyerowitz EM, Jiao Y
(2019) A gene expression map of shoot
domains reveals regulatory mechanisms. Nat
Commun 10:141
42. Reynoso MA, Blanco FA, Bailey-Serres J,
Crespi M, Zanetti ME (2013) Selective recruitment of mRNAs and miRNAs to polyribosomes in response to rhizobia infection in
Medicago truncatula. Plant J 73:289–301
43. Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S,
Masson H, Inagaki S, Federici F, Sinha N,
Deal RB, Bailey-Serres J, Brady SM (2014)
Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell
type-specific gene expression and function
using tomato as a model. Plant Physiol
166:455–469
44. Zhao D, Hamilton JP, Hardigan M, Yin D,
He T, Vaillancourt B, Reynoso M,
Pauluzzi G, Funkhouser S, Cui Y, BaileySerres J, Jiang J, Buell CR, Jiang N (2017)
Analysis of ribosome-associated mRNAs in
rice reveals the importance of transcript size
and GC content in translation. G3 (Bethesda)
7:203–219
45. Castro-Guerrero NA, Cui Y, Mendoza-Cozatl
DG (2016) Purification of translating ribosomes and associated mRNAs from soybean
(Glycine max). Curr Protoc Plant Biol
1:185–196
46. Reynoso MA, Juntawong P, Lancia M, Blanco
FA, Bailey-Serres J, Zanetti ME (2015) Translating ribosome affinity purification (TRAP)
followed by RNA sequencing technology
(TRAP-SEQ) for quantitative assessment of
plant translatomes. Methods Mol Biol
1284:185–207
47. Reynoso MA, Pauluzzi GC, Kajala K,
Cabanlit S, Velasco J, Bazin J, Deal R, Sinha
NR, Brady SM, Bailey-Serres J (2018) Nuclear
transcriptomes at high resolution using
retooled INTACT. Plant Physiol 176:270–281
48. Townsley BT, Covington MF, Ichihashi Y,
Zumstein K, Sinha NR (2015) BrAD-seq:
breath adapter directional sequencing: a
streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA
library construction. Front Plant Sci 6:366
49. Blankenberg D, Gordon A, Von Kuster G,
Coraor N, Taylor J, Nekrutenko A (2010)
Manipulation of FASTQ data with Galaxy. Bioinformatics 26:1783–1785
50. Trapnell C, Pachter L, Salzberg SL (2009)
TopHat: discovering splice junctions with
RNA-Seq. Bioinformatics 25:1105–1111
51. Kim D, Langmead B, Salzberg SL (2015)
HISAT: a fast spliced aligner with low memory
requirements. Nat Methods 12:357
52. Trapnell C, Williams BA, Pertea G,
Mortazavi A, Kwan G, van Baren MJ, Salzberg
SL, Wold BJ, Pachter L (2010) Transcript
assembly and quantification by RNA-Seq
reveals unannotated transcripts and isoform
switching during cell differentiation. Nat Biotechnol 28:511
53. Thorvaldsdottir H, Robinson JT, Mesirov JP
(2013) Integrative genomics viewer (IGV):
high-performance genomics data visualization
and exploration. Brief Bioinform 14:178–192
54. Kang YJ, Yang DC, Kong L, Hou M, Meng
YQ, L W, Gao G (2017) CPC2: a fast and
accurate coding potential calculator based on
sequence intrinsic features. Nucleic Acids Res
45:W12–W16
55. Wang L, Park HJ, Dasari S, Wang S, Kocher JP,
Li W (2013) CPAT: coding-potential assessment tool using an alignment-free logistic
regression model. Nucleic Acids Res 41:e74
56. Hezroni H, Koppstein D, Schwartz MG,
Avrutin A, Bartel DP, Ulitsky I (2015) Principles of long noncoding RNA evolution derived
from direct comparison of transcriptomes in
17 species. Cell Rep 11:1110–1122
472
Soledad Traubenik et al.