We have pieced together the playbooks!

I'll be presenting our research progress next week at the 35th New Phytologist Symposium in Boston. The theme of the conference is "The genomes of forest trees: new frontiers of forest biology" and I couldn't be happier to share with and learn from the experts in attendance. I'm also excited to share some of the results with you backers who are critical to the success of the project.

I'll return to the football analogy (along with others) to explain our progress. We took a snapshot of the transcripts from our resistant and susceptible ash trees. These transcripts are the plays that each tree calls to defend itself from the attacking beetles, and our snapshot captures which plays are called and how often. In order to read the plays/transcripts (which are actually microscopic stringy nucleic acid molecules inside plant cells) we had to chop them up into tiny pieces, read those pieces, and then put them all back together again.

 

To do this we used "shotgun sequencing," described in the clip below (Substitute "transcriptome" for "genome" and "ash tree" for "human". Also, the problematic repeats are less common in transcriptomes than they are in genomes).

So we know the plays that were called by each ash species, we have the sequences of their transcripts. We're still working on quantification --that is calculating how often each of the plays were called. Some of the results I'm presenting at the meeting are comparisons of our playbooks with those put together by other researchers working on other species of ash.

 

This figure comes right of the poster I'm presenting, you're not getting anything watered down. The column labeled "Genes" corresponds to what I've been calling "transcripts" or "plays". These are unique sequences being expressed by the trees. You can see that the numbers of genes we've identified in our playbooks are very similar to the numbers from European ash put together by the Open Ash DieBack team in the UK. The column "Transcript isoforms" refers to variations of the genes. Isoforms are like option plays in football that come from the same play call, but end up being expressed differently on the field depending on conditions. So naturally, there are more possible play outcomes than there are plays. Again, we're pretty consistent with European ash and with green ash put together by The Hardwood Genomics Project. This consistency is encouraging and bodes well for our ongoing analysis

I'll update you again once we have finished the quantitation and figured out which plays resistant Manchurian ash are calling more often than susceptible white ash.

Until then,

David