tpj12623-sup-0009-Legends

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Supporting Information Legends
Figure S1. Phylogenetic analysis of HAG co-regulators from maize. a), b), c), The
ZmHAG family of GNC5-related histone acetyltransferases can be subdivided into three
subfamilies named GCN5, ELP and HAT1 respectively (Liu et al., 2012). Each of the
cloned HAG maize co-regulators was scanned for the presence of an acetyl-CoA binding
site using the Conserved Domain database (CDD). This region (approximately 75 to 90
amino acids) was then used as the operational taxonomic unit for phylogenetic analysis.
Related proteins were aligned using CLUSTALW using default parameters. The
phylogenetic tree was exported in Newick format and displayed using FigTree V1.4.0.
Raw branch lengths are shown to scale.
Figure S2. Phylogenetic analysis of AUX/IAA co-regulators from maize. Full length
amino acid sequences were aligned using MUSCLE using default parameters (VTML
200 substitution matrix with a gap opening penalty of -2.9 a gap extension penalty of 0).
The maximum number of iterations was 8 with UPMGB as the cluster method and
CLUSTALW for sequence weighting. The initial distance measure was Kmer 6-6 and
Kimura % identity used for later iterations. The phylogenetic tree was exported in
Newick format and displayed using FigTree V1.4.0. Raw branch lengths are shown to
scale.
Figure S3. Nucleotide sequence alignments showing the codon usage of the three
synthetic codon optimized constructs for GRMZM2G162434, GRMZM2G001875,
and GRMZM2G051793. Nucleotide sequences for the codon optimized constructs were
retrieved from the sequence files provided by GeneArt®. Native sequences were
retrieved from a CDS library of B73 RefGen_v2. Multiple alignments were then
generated amongst the native, maize optimization, yeast optimization, and hybrid
optimization CDS using SeqMan™ of the DNASTAR bioinformatics suite.
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Figure S4. Workflow describing the cloning process used to generate the maize
TFome collection.
Table S1. RNA-Seq data used for the validation of gene models. Reads from 24
publically available RNA-Seq runs (Table S1a) and reads from 23 published and
unpublished RNA-Seq runs (Table S1b) generated in our lab or through collaborations
were used for our alignments. Reads from each sample were aligned to the B73
RefGen_v2 using Tophat. Next, each alignment file was merged using SAMtools.
BEDtools was then used to intersect the merged alignment against the genomic coordinates of our genes of interest. The .bam files were then loaded into Integrative
Genomics Viewer for visualization.
Table S2. Table shows the percentage of clones successfully amplified from a variety
of maize tissues by RT-PCR (n= 244).
Table S3. Sequence discrepancies between maize TFome clones and B73 RefGen_v2
models.
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