Table 1.
Levels of genome-wide functional annotation within the FAASG framework
| Class of variation | Context | Origin of data | Goal |
|---|---|---|---|
| Genomic sequence | Phylogeny-wide | Comparative analysis | Define fixed substitutions across species including for WGD gene duplicates. Assign to different classes: exonic, intronic, regulatory, synonymous vs. non-synonymous; radical vs. conservative non-synonymous and divergent from ancestral state Identify differences in structural genomic variation among species and describe its evolution Associate sequence/structural genome variation with epigenetic, transcriptomic and proteomic variation |
| Genomic sequence | Population-level | Genome-resequencing | Define SNPs and structural genome variation within species. Assign to different classes: as above Associate sequence/structural genome variation with epigenetic, transcriptomic and proteomic variation |
| Epigenetic (DNA methylation) |
Phylogeny-wide and population level | Assays described in Additional file 1: Table S1. | Generate DNA methylome maps and define their regulation across tissues, developmental stages and common-garden physiological manipulations Associate changes in methylation with all forms of genomic, transcriptomic, proteomic and other classes of epigenetic variation |
| Epigenetic (histone modifications) |
Phylogeny-wide and population level | Assays described in Additional file 1: Table S1 | Define a range of histone marks and their regulation across tissues, developmental stages and common-garden physiological manipulations Associate variation in histone marks with all forms of genomic, transcriptomic, proteomic and other classes of epigenetic variation |
| Epigenetic (chromatin biology) |
Phylogeny-wide and population level | Assays described in Additional file 1: Table S1 | Generate maps of DNA accessibility and define their regulation across tissues, developmental stages and common-garden physiological manipulations Associate changes in chromatin structure with all forms of genomic, transcriptomic, proteomic and other classes of epigenetic variation |
| RNA expression | Phylogeny-wide and population level | RNAseq - potentially stranded protocols (see Additional file 1: Table S1) | Define expression of miRNA, mRNA and non-coding RNA across adult tissues, developmental stages and common-garden physiological manipulations [1] Associate transcriptomic variation to all forms of genomic, epigenetic and proteomic variation |
| Protein level | Phylogeny-wide and population level | Various possible mass spectrometer platforms – bottom up approach | Define proteome across tissues, developmental stages and common-garden physiological manipulations Associate proteomic variation to all forms of genomic, transcriptomic and epigenetic variation |