Table 1.
Statistical summary of the Trinity de novo transcriptome assembly of Hypoxis hemerocallidea.
Fig 1.
Gene ontology (GO) level 2 classification and proportion of assembled transcripts from Hypoxis hemerocallidea.
Classification is grouped under the GO domains: ‘cellular component’, ‘molecular function’ and ‘biological process’.
Fig 2.
A) General representation of the annotated transcripts. B) Pathway groups integrated into ‘metabolism’ C) Pathways grouped under three categories of metabolism’: ’Metabolism of cofactors and vitamins’, ‘Biosynthesis of other secondary metabolites’ and, ‘Metabolism of terpenoids an polyketides’.
Fig 3.
Heatmap of the differentially expressed transcripts between the tuber, leaf and flower tissues of H. hemerocallidea.
The heatmap was generated with a p-value of 0.05 and a one-fold change cut-off for the false discovery rate of the differential expression analysis performed with edgeR. The 1st cluster of 823 transcripts was found to be upregulated in the leaf tissue with a mean log2(fpkm+1) of 2.2. A similar mean is exhibited by the 34 transcripts upregulated in the corm tissue (2nd cluster). However, the mean log2(fpkm+1) of the upregulated transcripts in the flower tissue (3rd cluster) is double that of the tuber and leaf upregulated transcripts. Line plots depict the expression levels of transcripts for each of the three clusters.
Fig 4.
Proteomic confirmation of upregulated transcripts in the leaf, flower and corm tissues.
The proteomic extraction methods are exhibited proportionally in Euler diagrams for A) leaf, B) Flower and C) Corm. A Venn diagram is included in C to display the 2 transcripts identified in all proteomic extracts as well as upregulated transcriptomically.
Fig 5.
Overview of secondary metabolism.
Blue squares indicate assembled transcripts. The 6-point line graphs with a yellow circle next to them are plots of differentially expressed transcripts in duplicate for the corm, leaf and flower tissues with log2(FPKM +1) on the vertical axis. The 3-point line graphs that are not otherwise marked, represent the qualitative detection of proteins in the corm, leaf and flower tissues.
Fig 6.
Red squares indicate assembled transcripts. The 6-point line graphs with a yellow circle next to them are plots of differentially expressed transcripts in duplicate for the corm, leaf and flower tissues with log2(FPKM +1) on the vertical axis. The 3-point line graphs that are not otherwise marked, represent the qualitative detection of proteins in the corm, leaf and flower tissues.