Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility
Botany Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
BMC Genomics 2013, 14:342 doi:10.1186/1471-2164-14-342Published: 23 May 2013
Additional file 1:
Supplemental Methods 1. Preliminary confirmation of hybrid identity of F1 plants via PCR based genetic markers.
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Additional file 2: Table S3:
Genetic positions of reference transcripts showing identity to sequenced markers appearing on a map of H. annuus derived from recombinant inbred lines from the population RHA280 × RHA801 (unpublished).
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Additional file 3:
Supplemental Methods 2. Perl script used to extract informative single nucleotide variants for analysis of allelic bias in hybrid transcript accumulation.
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Additional file 4: Figure S1:
Venn diagrams showing overlap between full (all data) and reduced (minus outlier samples HA89.9 and F1.TA) analyses.
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Additional file 5: Table S1:
All reference transcripts showing at least one significant difference in analyses of species differences between H. annuus cmsHA89 and H. petiolaris Pet2152 or analyses of transgressive, non-additive, high variance, or allele-biased transcripts in F1 hybrids. ‘REFERENCE’ identifies the reference contig. ‘LENGTH’ gives the length of the reference contig in bases. Black or grey symbols within the following columns indicate whether the specified difference was statistically significant in both full and reduced analyses (black/bold) or only a single analysis (grey). For “TRANSGRESSIVE” and “NON-ADDITIVE” transcripts, '▲'indicates that F1 samples showed a mean transcript accumulation greater than observed for either parental accession; '▼' indicates lower levels of transcript in F1 samples. For “NON-ADDITIVE” transcripts, '●' indicates that F1 transcript accumulation was intermediate relative to parental accessions. For “ALLELIC BIAS” and “SPECIES DIFFERENCE”, 'A' and 'P' indicate that higher transcript accumulation was observed for the H. annuus or H. petiolaris allele/accession, respectively. For “HIGH CV”, '●' indicates a contig showing a coefficient of variation among F1 samples that is ≥ 2. “TAIR10” provides the best nucleotide BLAST hit to the TAIR10 genome assembly (http://www.arabidopsis.org webcite); “no hit” indicates no results with e-value < e-10. “UNIPROT” provides the uniprot id for the best BLASTX hit against the UniProt Knowledgebase, release 2012_08. “description” provides an abbreviated annotation of gene function.
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Additional file 6: Table S2:
Transcripts showing transgressive levels of accumulation in F1 hybrids in either full or reduced analyses. Mean RPKM per accession (A = H. annuus cmsHA89, H = F1 hybrid, P = H. petiolaris Pet2152) are provided for both full (“full”) and reduced (“red”) analyses. ‘SIG’ indicates whether a given transcript shows significant transgression in ‘FULL’, ‘REDUCED’, or ‘BOTH’ analyses, with ‘FULL(TA)’ indicating transcripts that were transgressive in full analyses due to inflation of the F1 mean transcript estimates by the sample F1.TA. ‘Transgressive’ indicates whether F1 transcript levels were determined to be high or low compared to parental accessions. ‘Summary_Annotation’ summarizes the hypothesized gene function based on BLAST-identified similarity. Annotation of the best protein BLAST hit is provided, along with the GenBank identifier and e-value for the BLAST hit, in subsequent columns.
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Additional file 7: Figure S2:
Addendum to Figure 4b, showing full data (outlier samples HA89.9 and F1.TA were not included in the main manuscript figure). This heatmap shows z-score normalized transcript accumulation for 166 reference contigs with CV > 2 within F1 samples. Samples from individual plants are shown in horizontal rows. Hierarchical clustering estimated from Spearman correlation coefficients for pairwise contig (x-axis) and sample (x-axis) distance matrices. The colored bar along the top edge indicates assignment of transcripts to GO Biological Process groups, with prominent categories: green (cell cycle/mitosis), yellow (histones/chromatin modification), blue (metabolism), red (stress/defense), and pink (transcription factors/signaling)
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