Table S1. Tissue sources of total RNA used for cDNA-primed genome amplification
Tissue
Genotype
Stress treatment
Reference
Shoot tip
WT 717
none
unpublished
Young stem (internodes 1-5)
WT 717
none
unpublished
Newly emerged leaf (LPI 0-1)
WT 717
none
unpublished
Mature leaf (LPI 15)
WT 717
none
Frost et al. 2012
Xylem (internodes 20-30)
WT 717
none
Frost et al. 2012
Bark (internodes 20-30)
WT 717
none
Frost et al. 2012
Mature leaf (LPI 15)
Transgenic 717 with RNAi-silenced Potri.002G106900
acute drought
Frost et al. 2012
Xylem (internodes 20-30)
Transgenic 717 with RNAi-silenced Potri.002G106900
acute drought
Frost et al. 2012
Bark (internodes 20-30)
Transgenic 717 with RNAi-silenced Potri.002G106900
acute drought
Frost et al. 2012
Root tip (distal 2 cm)
Transgenic 717 with RNAi-silenced Potri.002G106900
acute drought
Frost et al. 2012
Root tip (distal 2 cm)
Transgenic 717 with RNAi-silenced Potri.002G106900
recovery following
acute drought
Frost et al. 2012
Expanding leaf (LPI 5)
Transgenic 717 overproducing salicylic acid
heat
Xue at al. 2013
Xylem (internodes 20-40)
Transgenic 717 overproducing salicylic acid
none
Xue at al. 2013
Coarse root
Transgenic 717 overexpressing Potri.009G095100
nitrogen limitation
Babst et al. 2014
Expanding leaf (LPI 5-6)
Transgenic 717 overexpressing Potri.016G014500
none
unpublished
Root tip (distal 1 cm)
Transgenic 717 overexpressing Potri.016G014500
none
unpublished
none
unpublished
Pollen
P.
deltoidesa
a
P. deltoides pollen RNA was also included in order to diversify the transcriptome representation. Flowering branches were
provided by Randy Rousseau of Mississippi State University.
Babst BA, Chen H-Y, Wang H-Q, Payyavula RS, Thomas TP, Harding SA, Tsai C-J (2014) Stress responsive Populus
hydroxycinnamate glycosyltransferase modulates phenylpropanoid metabolism. Journal of Experimental Botany 65:4191-4200.
Frost CJ, Nyamdari B, Tsai C-J, Harding SA (2012) The tonoplast-localized sucrose transporter in Populus (PtaSUT4) regulates
whole-plant water relations, responses to water stress, and photosynthesis. PLoS ONE 7:e44467.
Xue L-J et al. (2013) Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state, but not growth in
transgenic Populus. Plant Cell 25:2714-2730.
Table S2. List of NGS datasets used in this study
SRA accession
Data type
Name
Sample code
SRP049825
PE100
Populus tremula x Populus alba 717-1B4 genome sequencing
All
SRP042117
PE100
Xylem transcriptome response of transgenic Populus with altered
tubulin expression
All
SRP041959
PE50
RNAseq analysis of SUT4-RNAi Populus
All
SRP059838
PE100
Populus defoliation experiment
All
SNP-calling
Mapping performance evaluation
SRP059838
PE100
Populus defoliation experiment
SRX1071040, SRX1071050,
SRX1071051
SRP041959
PE50
RNAseq analysis of SUT4-RNAi Populus
SRX547993-SRX547998,
SRX548011-SRX548016,
SRX548029-SRX548034,
SRX548047-SRX548052
SRP049825
PE100
Populus tremula x Populus alba 717-1B4 genome sequencing
SRX759988
SRP028935a
SE50
Transcriptional network study of Populus stem secondary growth
SRX337461
a
Liu L, Missirian V, Zinkgraf M, Groover A, Filkov V (2014) Evaluation of experimental design and computational parameter
choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. BMC Genomics 15:S3
Table S3. Identification of 717 genomic variants.
Data source
Program/variant-calling method
DNA-Seq
SHORE
Variant no.
Consensus
10,484,677
qVar
10,957,316
GATK
UnifiedGenotyper
10,128,808
HaplotypeCaller
1,189,782
RNA-Seq
Trinity & Samtools
1,319,112
NCBI mRNA
Samtools
10,886
Table S4. Number of expressed genes detected using the
two different genomes.
Ptr_v3
sPta717_v1.1
Difference
SE50
Leaf
22,213
22,770
557
Bark
22,783
23,408
625
Xylem
20,525
20,970
445
Leaf
22,435
22,906
471
Bark
22,995
23,542
547
Xylem
20,716
21,099
383
Leaf
21,303
22,179
876
Bark
21,936
22,910
974
Xylem
20,705
21,524
819
Leaf
21,538
22,383
845
Bark
22,234
23,027
793
Xylem
20,977
21,674
697
PE50
SE100
PE100
Genes with an FPKM ≥1 were considered expressed.
Table S5. Mapping rates of DNA-Seq and ChIP-Seq reads.
Genomic DNA Input
ChIP-Seq
Ptr_v3
sPta717
Ptr_v3
sPta717
Uniquely mapped
29.6%
39.5%
30.0%
40.4%
Multiply mapped
24.3%
25.6%
22.6%
23.8%
Unmapped
46.1%
34.8%
47.4%
35.8%
SE50 data from SRA accession no. SRP028935 (Liu et al. 2014 BMC Genomics
15:S3).
Table S6. Re-annotation of Affymetrix probe-sets using
the sPta717 genome
Grade
Ptr_v3
sPta717
A
43,497
32,241
B
5,909
14,601
C
286
266
E
8,654
11,085
R
2,905
3,058
Control
Total
162
162
61,413
61,413
Grades are defined according to Affymetrix. Grade A probe-sets had nine
or more probes matching to the annotated transcript. All other grades
had fewer than nine matching probes to the transcript, with B through R
signifying decreasing level of evidence in support of the annotation.