Lauren & Puneet
1. Determine sequence homology between blueberry, cranberry,grapefruit (contains flavonoids) etc.
It would be nice to find conserved motifs between these fruits which contain athnocyanins and flavonoids and discount the ones that are putatively involved in essential functions. Theoretically, this would leave us with candidate genes for athnocyanin/flavonoid activity. We would be limited by available genomes.
2. Myb transcription factor expression in various fruits (containing anthocynanins)
3. Repeats in the blueberry genome (WGDs?)
4. The different expression patterns: in the fruit vs root; different times of the day; different seasons; various environmental factors
5. What is the BAHD family of phenolic ATs (mentioned in proposal); check out cytochrome p450s and o-methyl-transferases.
The BAHD family of ATs are acyltransferases and contain, according to the grant proposal, the f2 conserved domain; apparently, researchers have found 94 putative BAHDs in Populis and 64 in Arabidopsis. It would be interesting to see if these sequences are conserved throughout athnocynanin containing fruits (of course, this would require obtaining the lignin, cranberry, etc. genome). Additionally, they talked about how there is some evidence that these enzymes are related to malonating athnocynanins.
In the proposal, they use grape to identify possible candidate genes for OMTs, ATs, Mybs, etc. in the blueberry using the grape genome (because they haven't diverged too much evolutionarily). This seems like a good strategy to do for other proteins/genes that are worth checking out e.g. ones involved in glucose metabolism and ATP sythesis?
6. ATP synthesis and glucose metabolism in blueberries.
7. The amount of t-RNA genes expressed in the blueberry
8. The number of introns, exons, transposable elements? What’s conserved?