Supplemental figures (titles and legends)
Figure S1. Length distribution of VS16 454-ESTs.
cDNA libraries were sequenced using the Roche/454 GS FLX system. EST
sequences were filtered and clipped (Material and Methods). The resultant 1.5
million ESTs were binned in 10 bp intervals for plotting.
Figure S2. Switchgrass genotype AP13 (a, b) and VS16 (c, d) node cultures on
media with antibiotics and fungicide.
Figure S3. Homology of switchgrass AP13 unitrancripts compared to reference
genome.
Unitranscript sequences of AP13 were BLASTed against transcript data of foxtail
millet (E-value < 10-5). The numbers of top hits per foxtail millet gene transcript
were plotted.
Figure S4. Assembly of subsets of ESTs and pooling strategy for PviUTs.
Six subsets of unitranscript sequences were produced separately. Major
parameters used in assembly are included in round brackets adjacent to the
programs (o, minimum overlap; p, minimum percent identity). Libraries and ESTs
in black boxes were generated in this project. Others in the colored boxes were
downloaded from NCBI without quality data. The length range and distribution of
PviUTs are shown in the histogram.
Figure S5. BLASTN E-values of PviUTs vs annotated foxtail millet transcript
sequences
Percentage number of total PviUTs were plotted over the top hit e-values (a).
PviUTs with e-values between 1.0E-10 and 1.00 were further plotted using
increment of 10-1, showing the e-value dropping off after1.0E-4.
Figure S6. Functional annotation of PviUTs using CDD.
Using the Conserved Domain Database (CCD) with BLASTX, significant domain
footprints were assigned to 66% of all PviUT sequences.
Figure S7. Switchgrass seed germination and time points for sampling.
Figure S8. Stages of switchgrass inflorescence development.
(a) Inflorescence meristem initiation, including rachis meristem (a1), primary
branch meristem (a2), secondary branch meristem (a3), and floral primordium
formation (a4); (b) Floret development; (c) Rachis elongation; (d) Panicle
emergence.
Figure S9. Dissection of switchgrass vascular fiber from an internode (a) and a
magnified view (b).
Figure S10. Signal intensity distribution of Affymetrix probe sets.
Data accumulated at the Noble Microarray Facility were pooled and normalized
before average signal intensity of each probe set was calculated. RNAs used
were isolated from multiple organs exposed to various growth conditions or
treatments. Five different Affymetrix cDNA chips were included. Log2transformed values were plotted.
Figure S11. Number of probe sets detecting transcripts from various switchgrass
organs.
Supplemental tables (tiles)
Table S1. Microbial sequence contamination and estimation of 454-EST-derived
consensus sequences.
Table S2. 454-EST assembly of VS 16 with different programs.
Table S3. Newbler assembly metrics of 454-ESTs of VS16 with different
parameter settings.
Table S4. EST assembly and sequence resources used for the switchgrass
unique transcript curation.
Table S5. Estimated transcript and transcriptome coverage of switchgrass
unitranscripts.
Table S6. Alamo-AP13 × Alamo (non-AP13) tissues included in the gene
expression atlas.
Table S7. Summary of transcript sequence sources of probe sets and
present/absent in the switchgrass gene atlas.
Table S8 Most stably-expressed switchgrass genes.
Table S9. Organ-enhanced genes.
Table S10. Putative phenylpropanoid-monolignol biosynthesis genes and
normalized average transcript levels.
Table S11. Candidate phenylpropanoid-monolignol biosynthesis pathway genes
in switchgrass and expression in 24 organs or tissues.