New subject: [ROSEXEC-LIST] Fwd: Bryon's Executive Summary Assignments

8 Mar 2011

      Sorry if you've received this more than once. I sent it yesterday and it seems to have bounced.
Bryon
Begin forwarded message:
...
From: Bryon Sosinski bryon_sosinski@ncsu.edu
Date: March 7, 2011 4:49:37 PM EST
To: Jay Norelli Jay.Norelli@ARS.USDA.GOV, rosexec-list@bioinfo.wsu.edu
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.

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.

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.

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.
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."
Bryon
On Feb 24, 2011, at 6:21 PM, Norelli, Jay wrote:
...
Byron,
Please develop bulleted revision suggestions for “Define and exploit the Rosaceae genome” section of the Executive Summary.
Current text:
Define and exploit the Rosaceae genome<image001.gif>
Comprehensive analyses of Rosaceae genomes combined with comparative and functional genomics will provide the basis for understanding the complex biological processes underlying the array of diverse and unique traits seen in this family. This initiative will maximize knowledge transferability among the breadth of rosaceous crops, while concurrently developing key crop-specific resources. Sequencing peach (Prunus) as a ’reference’ species while concurrently obtaining skim sequence of strawberry (Fragaria) and apple (Malus) are high priorities. Sequencing will be followed by the development of resources and tools optimized for gene and regulatory element discovery, transcriptome analysis, and characterization of epigenetic influences. High-density genotyping and polymorphism discovery will accelerate forward genetic approaches and provide insight into genome evolution. Functional genomic approaches will exploit tractable systems and target physiological and developmental pathways contributing to key crop attributes. Collectively this approach will streamline discovery of beneficial genes, leading to sustained improvements in fruit quality and plant productivity throughout the range of rosaceous crops.
·         develop bullet points for suggested change/revision/addition/deletion for your assigned section
·         Proposed additions should be balanced with proposed deletions
·         DEADLINE for distribution  to RosEXEC is Monday, March 7, 2011
·         You will distribute your suggestions directly to RosEXEC via email as soon as you have it available.  Email should include 1) current text, 2) bulleted suggestions and 3) request for feedback via email before March 16 .
·         Responses received should be forwarded to other members of revision committee.
Thanks,
Jay
John (Jay) Norelli
Research Plant Pathologist
USDA-ARS, Appalachian Fruit Research Station
telephone: (304) 725-3451 x264
email: jay.norelli@ars.usda.gov
fax: (304) 728-2340
address: 2217 Wiltshire Road
              Kearneysville, WV  25430