More replies to NAASC letter

Joe Ecker jecker at ATGENOME.BIO.UPENN.EDU
Mon Jun 6 08:44:57 EST 1994


Dear Colleagues,

Below are several more responses to the North American Arabidopsis Steering
Committee letter regarding priorities for the Arabidopsis genome research 
project.  If you have not yet responded, but plan to do so, please post 
your response ASAP so that your comments can be considered during the NAASC 
workshop on June 8 & 9.

Community input is an important part of this process and we would 
like to thank those of you that have taken time to carefully consider these 
issues and respond. 

Sincerely,

Joe Ecker (for the NAASC)


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 RESPONSE # 13

 Many labs are currently sequencing their favourite at genes, this is tedious 
and is taking time and resources away from doing scientific experiments.  
In addition, there are many grad students whoes experinece in plants ammounts 
to  a lot of sequencing and some experience with northerns.
With this in mind, perhaps there could be some provision for the (presumably
worthwhile) genes in hand to be sequenced  as a prime goal of any 
random sequencing project.  I have not thought through the issues of timing of
release of this information, but believe these issues could be addressed.
I feel strongly that current plant biology is hampered by laborious techniques
(transformtion of at would be another example, but the improved in-planta 
methods may have overcome this burden to a large extent), and
that any field wide financing would be best directed towards getting 
the maximum experiments done.
thats my two cents worth,
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RESPONSE # 14

1. Do you think that we are ready to begin some level of directed genome
sequencing in the US?
I think it's not the time now to start sequencing the entire genome of arabidop
The completion of the physical maps and a "high density physical map" should 
have highest priority. But a limited sequencing project of about 1Mb would
give us some insight into the genome structure of Arabidopsis. There should be
enough mapped contigs of this size by now.
2. How important is genome sequencing in terms of funding priorities (vs.placing cDNAs on the map, completion of the physical map, adding more
PCR-based markers to the map, etc.)?
In my opinion the highest priority should have the mapping of the Ara genome,
then the sequencing and mapping of cDNA clones. The genomic sequencing should
have third priority. I would prefer full length sequenced cDNA clones over 
sequencing the whole genome.
3. Who should support systematic genome sequencing if it is a big-$ effort?
USDA. But if there is monies from other agencies it could be a concerted effort
financed by different agencies.
4. What impact on Arabidopsis research will be incurred if sequencing does not
begin today (in 2 years; in 5 years,  in 10 years)?
in 2 years: no genomic sequencing program would have little to no impact
in 5 years: mapping and cDNA sequencing projects should be finished and a genomic sequencing program should be on the way.
in 10 years: the complete genomic sequence of Arabidopsis should be completed
5. What type of organizational model for genome sequencing would you support:
sequencing centers vs. individual interested labs?
sequencing centers. individual labs are just a waste of resources for 
megaprojects.
6. What quality standards would you expect for the sequence: high or low
accuracy (high accuracy = higher cost)?
high accuracy even at higher cost.
7. ANY SPECIFIC OR GENERAL COMMENTS THAT YOU WOULD LIKE TO MAKE!
I hope that the next generation of sequencers and automation will cut the costs
for megasequencing remarkebly. Right now there are projects for the Arabidopsis
community that are more important than genomic sequencing at this point. 
mapping the genome, saturated insertion mutagenesis, sequencing of cDNAs.
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RESPONSE # 15

1. Do you think that we are ready to begin some level of directed genome 
sequencing in the US?  

Yes.  It's clear that for many situations a good physical map is sufficent,
however we have the opportunity to create a tremendous resource for all
plant biologists by increasing our resolution of a plant genome to the
level of DNA sequence.  Enough of the genome is covered in cosimid and
lambda contigs, not to mention YACs, to allow full scale sequencing to
begin.  It seems that in many ways the project is at a critical point, and
delaying may eliminate it from high priority category of the various
funding agencies...we may lose the chance to get this off the ground
altogether.  Already it seems that some of the "genome initiative" momentum
of 5 to 7 years ago, when the first generations maps were being created and
published, is being lost...at least in comparison to yeast, C. elegans,
mouse and humans.  In my opinion the community needs to get behind this now
if it is going to proceed.   

2. How important is genome sequencing in terms of funding priorities (vs. 
placing cDNAs on the map, completion of the physical map, adding more 
PCR-based markers to the map, etc.)?	 It's time to sequence.  The map will
"fill up" with additional markers as needed; the marker resolution (both
PCR-based and RFLPs) is dense enough to allow linkage studies and cloning
projects to be carried out.  

3. Who should support systematic genome sequencing if it is a big-$ effort?
Of course it will be a big money effort.  I would suggest a special
appropriation to USDA and DOE, jointly, hopefully to take advantage of some
of the current DOE genome center expertise.  Also, it seems that some
industries may be interested.  Rumor has it that private money has been
discussed to initiate sequencing the genome of a major crop plant.

4. What impact on Arabidopsis research will be incurred if sequencing does 
not begin today (in 2 years; in 5 years,  in 10 years)?  As I stated above,
we may lose a valuable window of opportunity if we don't start now. 
Obviously we could still be crawling to genes in 5 years without this.  We
could also lose important information on genome organization that could
indicate the basis for position efffects on transgenes, and ways to get
around the position-effect problems.  and more....


5. What type of organizational model for genome sequencing would you 
support: sequencing centers vs. individual interested labs?  a
hybrid...individual labs to organize regions to be sequenced and to take
responsibility for accuracy, etc, and centers to generate the sequence. 
clone order, accuracy, etc would be reviewed by the lab in charge of a
particular region, and they would work in close association with the
sequencing center.

                        
6. What quality standards would you expect for the sequence: high or low  
accuracy (high accuracy = higher cost)?high accuracy will be cheaper in the

long run    High accuracy...if we do this "wrong", we'll really regret in
the future for biological, experimental, and political reasons. 
                        			                                      
7. ANY SPECIFIC OR GENERAL COMMENTS THAT YOU WOULD LIKE TO MAKE!

just that if there is a push to make this happen it would be good to know
that the entire North American committee is behind it, and is willing to
lobby for it both within the Arabidopsis community and with the funding
agencies.  while this is a critical piece of research for all of us, it may
be hard to sell.  




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