Text below from: Colle, M. et al. 2019. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience
RNAseq experiments included in this analysis include plant tissue samples (flower bud, flower at anthesis, flower post- anthesis, young shoot, leaves treated with methyl jasmonate, small green fruit, expanding green fruit, pink fruit, ripe fruit and salt-treated and untreated roots). Additional experiments included three biological replicates each of berries at seven developmental stages (petal fall/cup, small green fruit, expanding green fruit, pink fruit, purple reddish fruit, purple unripe fruit and blue ripe fruit).
Counts of uniquely mapping reads were generated through HTSeq for all 35 RNAseq datasets. To construct the gene co-expression network, genes that were not expressed or very weakly expressed (count < 5) in 30 or more conditions were first excluded from the analysis. The count data was then transformed into variance stabilized values using the variance stabilizing transformation (VST) function in DEseq. Pairwise correlations of gene expression was calculated using Pearson’s correlation coefficient (PCC) and mutual rank (MR). MR scores were transformed to network edge weights using geometric decay functions; five different co-expression networks were constructed based on different rates of geometric decay. Edges with PCC < 0.6 or edge weight < 0.01 was excluded. For each network, modules of co-expressed genes were detected using ClusterONE v1.0 using default parameters, and modules with Pvalue > 0.1 or quality score < 0.2 were excluded. The results from all co-expression networks were then combined by collapsing modules into metamodules of nonoverlapping gene sets.
Our analysis identified 1988 metamodules of co-expressed genes, of which, 428 metamodules contained at least one of the 57 Pfam domains that have been previously categorized as associated with specialized metabolic pathways in plants. Our analysis revealed that 142 of 428 metamodules were more highly expressed in developing fruit compared to other plant tissues. Some metamodules showed clear trends of being highly expressed during either early or late fruit development. For example, METAMOD00377 is expressed early in fruit development and contains homologs to known anthocyanin genes OMT, HCT, PAL, HQT as well as 31 homologs to known transcription factors. In contrast, METAMOD01221 is expressed late in fruit development and contains homologs of HCT, TT19, UFGT, OMT and contains 10 homologs to known transcription factors. Moreover, we also examined metamodules for genes associated with other biosynthetic pathways which impart unique blueberry fruit characteristics. We identified two metamodules where genes appear to be co-regulated. Metamodule METAMOD00377 contains Pfam domains associated with terpene, saccharide, and alkaloid specialized metabolism and METAMOD01221 which contains terpene and saccharide metabolism. These metamodules contained genes that are differentially expressed during fruit development. Overall, the developmental-specific expression patterns of key biosynthetic genes and their putative transcriptional regulators emphasizes the tight regulation of production, conversion and transport of precursor compounds that lead to the accumulation of antioxidant-related metabolites in blueberry.
Cite this work
Researchers should cite this work as follows:
- Wisecaver, J. H., Edger, P. (2019). Global coexpression analysis of genes in haplotype-phased genome of tetraploid blueberry.. Purdue University Research Repository. doi:10.4231/0FAA-GK65
The data files published here were created using R.