my comments below in red
Sorry if you've received this more than once. I sent it yesterday and it seems to have bounced.
Begin forwarded message:From: Bryon Sosinski <firstname.lastname@example.org>
Date: March 7, 2011 4:49:37 PM EST
Subject: Re: Bryon's Executive Summary Assignments
All,In addition to the comments that others have made, and to reinforce them in some cases, here's what I am thinking for this section of the Executive Summary:- In the context of having three rosaceous genomes, it is critical to perform detailed comparative studies (both micro and macro synteny) to evaluate gene copy number, presence or absence of pathways and their genes. This would provide a needed stepping stone for functional genomics. This would also ameliorate the need to deeply sequence another genome (e.g. rose or raspberry) in order to capture the genes, and provide the context for genome structure. agree
- Continue to develop at least one species' genome as a "reference genome" for the family (obviously I would propose peach due to the existing high level coverage and alignment). A reference genome is a key component for the above mentioned analyses, and is also important for the pursuit of "gene and regulatory element discovery, transcriptome analysis, and characterization of epigenetic influences" This is particularly true to do thorough epigenetics. agree, but mention the need of a reference genome for the most important genera of Rosaceae family
- The portion that deals with "High-density genotyping..." should be rewritten to discuss RosBREED (and the EU counterpart) in the development of markers, and the coordination of those projects that will presumably mean less redundancy etc. agree,
So I think what I just proposed is striking the 2nd and 3rd sentences, writing something dealing with a reference genome(s), and to promote comparative studies for the 2nd sentence. This would allow "cheap" sequencing for upcoming genomes. Discussing RosBREED et al. and coordination of those projects would be a substitute for the 3rd sentence. The final 2 sentences would remain largely unchanged. agree
Also, I did another quick skim of the entire document, and found little on standardized phenotyping. Therefore, I would argue that putting a line in here stating, "The availability and reliability of affordable high throughput phenotyping, is a critical consideration for conducting detailed functional genomics."
On Feb 24, 2011, at 6:21 PM, Norelli, Jay wrote:
Main Bioinformatics Laboratory at WSU
ROSEXEC-LIST mailing list