Cactus genome sequencing project

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pjiang
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Cactus genome sequencing project

Post by pjiang » Sat Mar 07, 2015 5:28 am

My name is Peng Jiang. I received my Ph.D. from department of horticulture, University of Georgia, USA. My research team is sequencing cactus genome with BGI now. I am writing this email for asking everyone who like cactus would like to support this project.

Cactus genome size is about 3Gb. Using high-throughput Illumina sequencing (paired-end, 150bp HiSeq 8 runs), we will generate 100 times coverage, which is 300 Gb data to assemble the Cactus genome. Furthermore, our genome analysis team will analyze sequencing data by ourselves, so the genome analysis fee and labor fee will not be included in this budget.

For detail of this project: https://experiment.com/projects/sequenc ... resistance

We are confident that cactus genome will be published on a top journal, such as Science, Nature, Nature Genetics or PNAS. (The orchid genome has just been published in Nature Genetics: The genome sequence of the orchid Phalaenopsis equestris). Several important plant genomes, such as tomato, cotton, and sorghum, have been sequenced by University of Georgia. Our team members have participated in those plant genome projects:
The tomato genome sequence provides insights into fleshy fruit evolution (Nature) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres (Nature)
The genome of the mesopolyploid crop species Brassica rapa (Nature genetics)
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome (Science)

If you have any question about the cactus sequencing project, please feel free to let me know at pjiang@uga.edu.
Thank you very much!
Sincerely,
Dr. Peng Jiang
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Aiko
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Re: Cactus genome sequencing project

Post by Aiko » Sat Mar 07, 2015 5:26 pm

pjiang wrote:I am writing this email for asking everyone who like cactus would like to support this project.
If you want support, please let us know what kind of help you need right here in your post.
Don't let us search for it on some website!
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gerald
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Re: Cactus genome sequencing project

Post by gerald » Sun Mar 08, 2015 3:19 am

I can understand why it is of interest to study the genetics of commercial plants & crops, but why cactus? Much as it is interesting for academic reasons, what else is there at stake?
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Chris43
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Re: Cactus genome sequencing project

Post by Chris43 » Sun Mar 08, 2015 3:14 pm

The link given suggests that the purpose of the genome mapping is to understand drought resistance. It seems that $2300 is the overall budget, of which $200 so far has ben pledged. It gives no insight into how this understanding might be used. Might such an understanding be useful for future food crop development? Given our changing climate, major crop producers should be very interested if it were. But that's not who this researcher is targeting.
I am left in doubt therefore as to the real benefit, though would be happy to be enlightened further.
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Re: Cactus genome sequencing project

Post by IanW » Tue Mar 10, 2015 2:42 pm

gerald wrote:I can understand why it is of interest to study the genetics of commercial plants & crops, but why cactus? Much as it is interesting for academic reasons, what else is there at stake?
Since when did academic reasons stop being a worthwhile reason for doing something in itself? Why does everything have to have a commercial purpose nowadays? Research for the sake of research is how we discover the unexpected, and producing additional data in this sort of area is never a bad thing - even if this guy doesn't do much more with the data himself, at least it's there, and can be used by other researchers looking into other aspects of that data in future.

So what's at stake? well it's simple, failure to advance science in this area, that's what. The bigger a library of genetic data we have, the better we can understand the natural world.
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Re: Cactus genome sequencing project

Post by graham » Wed Mar 11, 2015 12:47 pm

IanW wrote:Since when did academic reasons stop being a worthwhile reason for doing something in itself? ...
I agree entirely. The research is worthwhile just to increase our knowledge and understanding.

graham
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Re: Cactus genome sequencing project

Post by pjiang » Fri Mar 13, 2015 7:48 pm

Thanks for everyone's comments! GigaScience has published a guest blog about the cactus genome sequencing project, which could address most questions. If you have time, please have a look at it: http://blogs.biomedcentral.com/gigablog ... ty-cactus/
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gerald
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Re: Cactus genome sequencing project

Post by gerald » Sat Mar 14, 2015 10:56 am

Chris43 wrote:Given our changing climate, major crop producers should be very interested if it were. But that's not who this researcher is targeting.
Having read the blog link above, it looks like that is exactly what the researcher is targeting. Nothing wrong with that of course, it's a good idea.
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Re: Cactus genome sequencing project

Post by Apicra » Thu Mar 19, 2015 8:23 pm

It is indeed very difficult for ordinary folk to assess whether a request for money is worthwhile.

I therefore suggest people who wish to donate money for c&s research (& conservation), channel their precious money via our host organisation, the UK BCSS charity. Funding requests, like in this thread, are properly refereed by expert peers before approval. "Crowd funding" research seems an inappropriate idea to me.

Best wishes,
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Re: Cactus genome sequencing project

Post by IanW » Thu Mar 26, 2015 1:20 pm

Apicra wrote:I therefore suggest people who wish to donate money for c&s research (& conservation), channel their precious money via our host organisation, the UK BCSS charity. Funding requests, like in this thread, are properly refereed by expert peers before approval. "Crowd funding" research seems an inappropriate idea to me.
Pretending the BCSS offers peace of mind on this particular issue is utter nonsense given the fact that we've had people put in legitimate requests for conservation funds and get them denied without any kind of transparency behind the reasoning. Frankly, providing money via the BCSS offers no more or less assurance than using a crowd funding approach unless there's been a complete overhaul in the way the BCSS does thing in this area in the last year or two. At least this way you get to make the choice directly, rather than having it made for you by people who haven't in the past at least been willing to justify their decisions whilst at the same time making (what I hope are) jokes about using BCSS' conservation funds to fund their own personal jaunts to their favoured habitats.
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