RESEARCH COMMUNITY COMMENTS on
DRAFT WHITE PAPER

From: Mlsk55@aol.com
Sent: Tuesday, September 03, 2002 9:38 AM
Subject: Comments

The Committee for Soil Microbiology and Root Diseases considers it to be important that Biological control agents are included in the list for the Plant Associated microbes Genome Initiative. The organisms suggested by committee members at the Milwaukee Meeting were the biological control organism Burkholderia cepacia and Ralstonia solanacearum.
Regards
Margaret Smither-Kopperl
Past-Chair 
Soil Microbiology and Root Diseases Committee.
mlsk55@aol.com

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From: André Lévesque [mailto:levesqueca@agr.gc.ca]
Sent: Friday, August 30, 2002 1:32 PM
Subject: Plant-Associated Microbe Genome initiative

TO: The members of the Public Policy Board and Drafting Committee of the white paper

Thank you all for taking the leadership in this broad initiative and for helping our community making difficult decisions. I strongly support the suggestion by the mycology committee that broad coverage of the taxonomic groups should be considered when selecting genomes for sequencing. At the last APS meeting the Plant Pathogen and Disease Detection committee did discuss this genome initiative. It was pointed out that for approximately the cost of sequencing one genome it would be possible to sequence a few ubiquitous genes for all the known plant pathogens, biocontrol agents and their relatives. Our committee would support this kind of work which would link phylogenetically all the plant-associated microbe genomics efforts. The development of accurate diagnostic tools for biosecurity is mentioned in the white paper but this will not be possible unless we have extensive databases on a wide range of pathogens and their relatives. I understand that there are some initiatives for phylogeny of microbes but they do not have a plant pathology and detection focus. If well coordinated with existing initiatives, additional resources for this kind of "phylogenomic" work could lead to a very extensive coverage of plant-related microorganisms, providing the molecular data essential for the detection and ecological studies of plant pathogens.

Andre Levesque
Past Chair of Plant Pathogen and Disease Detection Committee
Agriculture and Agri-Food Canada
Ottawa, Ontario

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From: Louis Bernier [mailto:Louis.Bernier@rsvs.ulaval.ca

Sent: Friday, August 30, 2002 10:05 AM
Subject: Draft White Paper

Dear Colleagues,

First of all, I would like to thank the members of the committee for the excellent work they did putting together the APS White Paper on the Plant Associated Microbes Genome Initiative, and organizing the Forum and Discussion in Milwaukee. 

Overall, I think the White Paper is well written, with clear objectives and recommendations. Being a forest pathologist, I was glad to see that the White Paper acknowledged the continuing impact of pathogens on forest trees and ecosystems. My specific suggestion here would be to reiterate this acknowledgement in the section of the document listing the criteria that were used to develop "the list" (p. 6). Thus, I would suggest to mention specifically "forestry" in the first criterion (Economic importance...) and "forest pathologists" in the third criterion (Broad interest...).

Not surprisingly, other people have commented on the choice of species in the current list, particularly on the absence of under-representation of particular groups of microbes. I believe this is also true for pathogens of trees. While, this is not the appropriate time and place to recommend one's favourite tree pathogens, I wanted to inform you that the APS Forest Pathology Committee has set up a small subcommittee on microbial genomics which is currently gathering input from researchers in the international forest pathology community. We should be able to provide you with a number of candidate tree pathogens, along with the rationale for their inclusion in the list, in the near future.

Sincerely yours,
Louis Bernier 
Professeur titulaire et directeur 
Centre de recherche en biologie forestière (CRBF) 
Pavillon C-E-Marchand 
Université Laval 
Québec (QC) 
G1K 7P4
Téléphone: (418) 656-7655 
FAX: (418) 656-7493Courriel: Louis.Bernier@rsvs.ulaval.ca 


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From: Luis Eduardo Aranha Camargo [mailto:leacamar@carpa.ciagri.usp.br]
Sent: Thursday, August 29, 2002 3:52 PM
To: microbegenomics@scisoc.org
Subject: greetings from Brazil

Dear Sirs
I am part of a Brazilian group which is sequencing plant-associated
microbes (http://www@aeg.lbi.ic.unicamp.br/aeg/aeg.html). 

Currently, we have just finished the sequencing of Leifsonia xyli subsp. xyli. Thus I see the PAMG initiative as an opportunity to strengthen our collaborative projects with US-based labs and others around the world. I am looking forward to discuss ways our group could participate in what certainly will be a very interesting project with wide scientific implications. 
Sincerely
Luis E. Camargo
Dept. Plant Pathology
University of Sao Paulo
Brazil


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From: Dave Austin [mailto:daustin@pbigordon.com]

Sent: Thursday, August 29, 2002 2:33 PM
Subject: feedback

It seems that the sequencing of genes of microbes should be prioritized
by crop groups, and within crop groups.
i.e.: Food Crops
Vegetables
Fruits
Feed Crops
corn
soybeans
cotton
alfalfa
pasture grasses
Fiber crops
cotton
kenaf
Ornamental Crops
Turfgrassses
Shrubs
Trees
Thank you.
Best Regards.
Dave
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From: Nevin Dale Young 
Sent: Monday, August 19, 2002 3:12 PM
Subject: Comments and Suggestions

Dear Plant-Associated Microbe Genome Initiative:

Thank you for the opportunity to submit comments about the genome 
initiative. It is an exciting and important effort, and I hope you 
are successful.

Because I am a member of both the U.S. Legume Genomics Steering 
Committee and the M. truncatula Genome Sequencing Task Force, I have 
had the opportunity to participate in numerous planning sessions in 
the area of genomics research. Based on my experience, I have two 
suggestions to make the Plant-Associated Microbe Genome Initiative 
more successful:

1. It remains extremely important for the community to develop robust 
BAC-based physical maps combined with deep BAC-end sequencing -- even 
if the focus will be on shotgun genome sequencing. Without the 
scaffolding of a sequence-tagged physical map, it will be difficult 
to establish physical relationships among sequenced contigs. This 
would weaken the research community's ability to use the (shotgun) 
genome sequence for applications such as positional cloning or 
comparative genomic analysis.

2. Because sequence annotation is so challenging -- and so important 
-- the community may want to consider a new paradigm for this effort. 
Specifically, you may want to consider approaching a major, respected 
journal (Plant Pathology; MPMI) to establish policies in which 
biologically-based sequence annotation can be submitted for 
peer-reviewed publication, along the line already used in some 
journals for short communications or meeting reports. As an example, 
a research group interested in a specific gene family might undertake 
the annotation of all members of that family within a given organism 
or group of organisms. In the process, the group would receive 
publication credit, add value to the genome sequence for the research 
community, and potentially uncover new insights into the biology of 
that gene family.

Suitable peer review would be required, and a thoughtful method to 
integrate these submissions into public sequence databases would be 
needed.

Good luck on your effort to secure funding and establish an 
productive genomics community.

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From: bbmg+@osu.edu 

Sent: Friday, August 09, 2002 10:24 AM
Subject: Biocontrol Microbes for Genome Sequencing

Dear Colleagues,

Thank you for putting together such an excellent white paper on the Plant Associated Microbes Genome Initiative. The work is thorough and well constructed. However after reading the list at the discussion session held on microbial genome sequencing priorities at the 2002 APS meeting, it became clear that no support has yet been given to the need for genome sequencing of bacteria and fungi involved in the biological control of plant diseases. This is troubling to myself and a number of other scientists investigating the nature of biological control. Therefore, as head of the APS Biological Control Committee, I will be assembling a list of recommendations to your group for inclusion. As a committee we will solicit the input of a number of biocontrol researchers on the selection and prioritization of no more than 10 strains of biocontrol agents (bacteria, fungi, and viruses). We hope to have such a list assembled for you in the next two months. Will that be satisfactory?

Thank you for your time. Regards,
Brian

Dr. Brian B. McSpadden Gardener
Department of Plant Pathology
The Ohio State University, OARDC
1680 Madison Avenue
Wooster, OH 44691-4096
330 202 3565 PH
330 263 3841 FAX
bbmg+@osu.edu

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From: O. W. Barnett mailto:ow_barnett@ncsu.edu

Sent: Monday, July 08, 2002 3:16 PM
Subject: White Paper response

Kurt,
Thank you very much for your thoughts and suggestions about the white
paper on the Genomics Initiative. I would like to comment on a few of
your points.
ARS support. The Public Policy Board is making every effort to get
agricultural research funding in general increased, if possible
doubled. Whenever we request more money for agricultural research we
always include ARS in the mix. We also stress that we do not want to
hurt one area of agriculture funding to increase funding in any area.
Amount of request. Yes, the $500 million is a large amount compared
to most areas of agriculture funding. However, genomics is an area
that Congress is willing to fund. Compared with the human genome cost
this is a small amount to request. Only a third of this is designated
for sequencing, the rest would go toward putting the genomes to good
use through functional genomics. On sequencing, an average fungus
might cost $5 million to get a complete, trustworthy sequence. 
Nematodes might take about $10 million and Phytopthora about $20
million, with bacteria being less than fungi. Several sequences of
different fungi will be needed to begin to do good comparative genomics,
so $100 million by itself would not go very far.
Your comment will be taken seriously as the proposal is reworked in
light of all the comments. Thanks for caring enough to take the time
to write.
O.W.
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From: Kurt Leonard mailto:kurtl@umn.edu
Sent: Friday, July 05, 2002 9:25 AM

To the APS Public Policy Board:

While I certainly sympathize with the need for a Plant-Associated 
Microbe Genome Initiative, I had to shudder at the magnitude of the 
request and what it says about priorities in our science. If my 
reading of the USDA,ARS website on national programs is correct, 
there are about 130 to 150 hard money supported research projects on 
plant diseases in all of ARS. The average annual funding for each 
project including salaries and facilities maintenance is certainly 
well under $1 million per project. Do we really believe that the 
impact of the Plant-Associated Microbe Genome Initiative on future 
disease management funded at $100 million per year will equal or 
surpass the impact of all current ARS projects combined that receive 
hard money support? Can we reasonably expect that Congress will not 
react to APS support for such a huge funding shift by questioning the 
scientific community's support for ARS's present priorities in 
funding research on plant diseases? That is, wouldn't a reasonable 
member of Congress interpret APS support for the $500 million 
initiative as evidence that APS, at least, thinks that most of the 
money currently going to ARS projects would be more effectively spent 
on microbe genome research?

Traditionally, congressional support for plant disease research has 
been commodity oriented. It seems unlikely that Congress will 
support such an expensive initiative without asking serious questions 
about where the money will be spent and which agricultural 
commodities will benefit directly. I think that the list of microbes 
with highest priority for funding in the initiative should include 
the crops impacted and it should be presented without qualification 
rather than as an ad hoc listing that is subject to change between 
how and the time that the money is to be appropriated.

Kurt J. Leonard
Department of Plant Pathology
University of Minnesota
St. Paul, MN 55108, USA
kurtl@umn.edu
612-625-8194

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From: Jan Leach mailto:jeleach@ksu.edu

Sent: Tuesday, July 02, 2002 4:38 PM
Subject: Microbe Genome Initiative

Microbe Community:
How will the Plant-Associated Microbe Genome Initiative 'work' as an international project? That is, should this be on an organism by organism basis, a taxonomic group by group basis, or as the whole plant-associated microbe entity?
Jan Leach

© Copyright 2002 by
The American Phytopathological Society