Supplementary Material
Trans-acting small interfering
RNA4: key to nutraceutical
synthesis in grape development?
Christopher D. Rock
Department of Biological Sciences, Texas Tech University, Lubbock TX 79409-3131
Corresponding author: Rock, C.D. (chris.rock@ttu.edu)
Figure S1. The tasi-RNA TAS4b-3’-D4(-) triggers production of phasiRNAs from VvMYBA6 and VvMYBA7 in grape. (A) Cartoon
map of MYBA6 (GSVIVT01030822001, XM_002274956) and MYBA7 (GSVIVT01030819001, XM_002274986) mRNAs showing
the relative position of sense phasiRNAs found in eight sRNA libraries from various tissues (GSE34169 [1]; GSM458927-30 [S2];
GSE28755). Perfectly matched 21 nt species are shown mapped above and below the MYBA6 and MYBA7 mRNAs, respectively
(horizontal bars with phase register labels). Vertical arrows show predicted cleavage sites of TAS43’-D4(-) that set the register,
and the vertical bar (gray) shows predicted binding site of miR828 at the 3’ end of the second SANT (SWI3, ADA2, N-CoR and
TFIIIB) DNA-binding domain (black rectangles). (B) Watson-Crick complementary base pairing of Vvi-miR828a (gray) and three
isoforms (abc; black font) of Vvi-TAS43’D4(-) to VvMYBA6 and MYBA7 mRNAs. For miR828a, the MYBA7 mRNA nucleotide
differences from MYBA6 are shown above in uppercase gray bold where the changes improve binding affinity, and lower case
for changes that reduce affinity. For TAS43’-D4 isoforms listed below, the same rules apply. Vertical arrow indicates cleavage,
setting register for phasiRNA production. (C) Sum of normalized (Transcripts Per Million) perfect match 21 nt sense siRNA
reads (log scale) from eight libraries (one tendril, two leaf, two flower, two fruit, one mixed) mapping to VvMYBA6 and
VvMYBA7 as a function of 21 nt phase registers (vertical gray lines). Methods: Illumina sRNA-Seq datasets were downloaded
from NCBI (www.ncbi.nlm.nih.gov) and converted to “fastq” format with the Sequence Read Archive Toolkit application “fastqdump.”
The
datasets
were
pre-processed
with
“FastQC”
(version
0.10.1;
www.bioinformatics.babraham.ac.uk/projects/fastqc/) and adapters removed with “Cutadapt” [S3]. BOWTIE (version 0.12.8)
[S4] was used to map reads to V. vinifera sequences [S5] compiled from BLASTN [S6] searches performed at
www.phytozome.org (release 9.0) and at the NCBI Plant EST database.
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Figure S2. Normalized abundances of unique perfect match 21 nt Vvi-TAS4 siRNAs and 22 nt miR828 in eight different sRNA
libraries from different grape tissues. (A) Vvi-TAS4a. (B) Vvi-TAS4b. There were no D2 species found. (C) VVi-TAS4c. There
were no D3(-) species found. (D) miR828 and miR828* abundances. Legend on right shows tissue sources, from NCBI datasets
GSE34169 [S1], GSM458927-30 [S2], and GSE28755. miR828 activity directly gives rise to the primary TAS4 product (D1[+]),
whereas the 3’D4(-) effector for VvMYBA6 and VvMYBA7 cleavage directly sets the register for the observed VvMYBA6/7
phasiRNAs shown in Supplementary Figure S1. Thus, correlations of abundances for these two most abundant phased species
for highly expressed TAS4a and TAS4b across three tissues (leaf, flower, fruit) by two independent experiments (GSM45892730 [S2], and GSE28755) allows an assessment of the reproducibility of the quantitative method (relative Transcripts Per Million,
TPM) [S7]. Such analysis provides a means to infer by association the relative functionality of TAS4b-3’D4(-) isoform over
TAS4a-3’D4(-) for the resultant phasiRNAs shown in Suppl. Fig. S1C. Although TAS4c-3’D4(-) is predicted to bind VvMYBA6/7
with higher affinity than the TAS4b species (shown in Suppl. Fig. S1B), it is expressed at >500-fold lower levels and therefore
does not likely play a major role in the production of MYBA6/7 phasiRNAs.
Methods
The phylogenetic tree in Figure 3 was constructed using the PhyML and TreeDyn [S8] by the neighbor-joining method with full
length MYB amino acid sequences (www.phytozome.org) and the MUSCLE algorithm [S9] (http://www.phylogeny.fr). Figure 4
tangentially addresses the potential role of miR858 in regulation of MYBs associated with polyphenolic metabolism. MIR858
homologs have not been described for grape (although homologies can be found; data not shown), but in any case candidate
miR858 binding sites in VvMYBA6 and MYBA7 (at nt 354 and 342, respectively) are poor, with mismatches at nt 4-6 that argue
against function based on the known topology of miRNA:target duplexes and AGO structure.
Supplementary references
S1. Wang, C., et al. (2012) Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and
analysis of microRNA variations with bioinformatics. BMC Genomics 13, 122
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S2. Pantaleo, V., et al. (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and
degradome analysis. Plant J. 62, 960-976
S3. Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal; Vol 17,
No 1: Next Generation Sequencing Data Analysis. Available at:
<http://journal.embnet.org/index.php/embnetjournal/article/view/200>
S4. Langmead, B., et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol 10, R25
S5. Jaillon, O., et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Nature 449, 463 - 467
S6. Altschul, S.F., et al. (1990) Basic local alignment search tool. J Mol Biol 215, 403-410
S7. McCormick, K., et al. (2010) Experimental design, preprocessing, normalization and differential expression analysis of
small RNA sequencing experiments. Silence 2, 2
S8. Dereeper, A., et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucl Acids Res 36, W465W469
S9. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32,
1792-1797
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