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Old 08-04-2011, 11:10 PM   #1
gprakhar
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Default List of Plant whose Genome Assembly has been done

Dear All,

Is there any list or Database from where I can find out the names of the Plants whose genome assembly has been done.

I did a PubMed search but wanted a more comprehensive list.(same for SRA)

Thanking you,
Prakhar Gaur
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Old 08-05-2011, 12:23 AM   #2
jimmybee
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Quote:
Originally Posted by gprakhar View Post
Dear All,

Is there any list or Database from where I can find out the names of the Plants whose genome assembly has been done.

I did a PubMed search but wanted a more comprehensive list.(same for SRA)

Thanking you,
Prakhar Gaur
NCBI Taxobrowser will give you all available genome sequences for Plants. It does include Chloroplast and Mitochondrial sequences but those can easily be removed

http://www.ncbi.nlm.nih.gov/genome/?...;Organism:exp]
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Old 08-05-2011, 12:57 AM   #3
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Originally Posted by jimmybee View Post
NCBI Taxobrowser will give you all available genome sequences for Plants. It does include Chloroplast and Mitochondrial sequences but those can easily be removed

http://www.ncbi.nlm.nih.gov/genome/?...;Organism:exp]
Thanks for the reply.

This will only tell about the organisms whose Genome is available.
I want to know about the Plants whose Genome assembly has been done using NGS technologies.
Its a kind of Literature survey work I am doing as I have to chalk out our own strategy regarding this.

Have already done PubMed searches, but asking here just to be sure.

--
pg

Last edited by gprakhar; 08-05-2011 at 12:59 AM. Reason: grammar
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Old 08-05-2011, 01:50 AM   #4
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You might get some more info on the GOLD Genomes online database.
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Old 08-05-2011, 08:09 AM   #5
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Quote:
Originally Posted by gprakhar View Post
Dear All,

Is there any list or Database from where I can find out the names of the Plants whose genome assembly has been done.

I did a PubMed search but wanted a more comprehensive list.(same for SRA)

Thanking you,
Prakhar Gaur
Dear Prakhar,
Could you post your list here when you've completed it? Thanks.
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Old 08-05-2011, 08:55 AM   #6
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Two useful places to check for this might be the JGI:

http://www.jgi.doe.gov/genome-projects/

and the BMAP consortium (for the brassicaceae):

http://www.brassica.info/resource/sequencing/bmap.php
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Old 08-09-2011, 05:18 AM   #7
gprakhar
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Quote:
Originally Posted by colindaven View Post
You might get some more info on the GOLD Genomes online database.
Thank you for the suggestion.
I checked out the GOLD db, but it does not contain the kind of data I am looking for.(update by groups who did want their data to be there)
Additionally it looks like it has not been updated for a long time.


Regards,
--
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Old 08-09-2011, 05:27 AM   #8
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Quote:
Originally Posted by plattsa View Post
Two useful places to check for this might be the JGI:

http://www.jgi.doe.gov/genome-projects/

and the BMAP consortium (for the brassicaceae):

http://www.brassica.info/resource/sequencing/bmap.php
Thank you for the reply,
JGI provided lots of info and so did BMAP(only about the Brassicaceae family though)

Regards,
--
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Old 08-09-2011, 05:33 AM   #9
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Originally Posted by Joann View Post
Dear Prakhar,
Could you post your list here when you've completed it? Thanks.
Yes sure.

I have given up hope of finding a comprehensive list of Plants genomes sequenced using NGS technology.

And have decided to make one myself.
Only one question to the Admin, can we have a wiki like list for this???
As in a separate page for the list!
That way I will populate the list initially and then everyone can contribute.
A similar thing for others(eg. vertebrates) will also do good for the community.

--
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Old 08-09-2011, 07:17 AM   #10
heartleaf_nettle
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I personally found this list very helpful:

http://synteny.cnr.berkeley.edu/wiki..._plant_genomes

Best wishes!
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Old 07-08-2013, 11:09 AM   #11
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I've been expanding this page, but is it complete?

http://en.m.wikipedia.org/wiki/List_..._plant_genomes

Thanks for any feedback or edits,
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Old 07-08-2013, 11:22 AM   #12
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We've recently published some 'partially' assembled crucifer genomes (scaffolds go up to 16MBase) and there may be a couple of other published genomes used in the paper as well that you may/may-not not have:

http://www.nature.com/ng/journal/vao...s/ng.2684.html
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Old 07-08-2013, 04:37 PM   #13
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Quote:
Originally Posted by dan View Post
I've been expanding this page, but is it complete?

http://en.m.wikipedia.org/wiki/List_..._plant_genomes

Thanks for any feedback or edits,
A good number of those genomes have not been assembled or annotated. You'll probably need to either redefined what you have suggested as a sequenced genome. Currently the page says "This list of sequenced plant genomes contains plant species known to have publicly available complete genome sequences that have been assembled, annotated and published. Unassembled genomes are not included, nor are organelle only sequences".

Maybe you should add a column with the relative "completeness" of each genome? E.g. Rice is quite complete (assembled into chromosome pseudomolecules, annotated well etc, whereas the Triticum species have little annotation and have not been assembled into anything like a chromosome).

Otherwise this is a great resource. Thanks for updating
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Old 07-10-2013, 01:40 AM   #14
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Quote:
Originally Posted by jimmybee View Post
Maybe you should add a column with the relative "completeness" of each genome? E.g. Rice is quite complete (assembled into chromosome pseudomolecules, annotated well etc, whereas the Triticum species have little annotation and have not been assembled into anything like a chromosome).
Absolutely agree. Actually that was my original intention when I started work on this page, but I got side-tracked ;-)

If I add the column, will you help populate the data? I figure we should use the standards linked here:
http://en.wikipedia.org/wiki/Talk:Li...mbly_status.3F

Many thanks,
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Old 07-10-2013, 02:17 AM   #15
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Quote:
Originally Posted by dan View Post
Absolutely agree. Actually that was my original intention when I started work on this page, but I got side-tracked ;-)

If I add the column, will you help populate the data? I figure we should use the standards linked here:
http://en.wikipedia.org/wiki/Talk:Li...mbly_status.3F

Many thanks,
Absolutely. I'll populate some info tonight
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Old 07-10-2013, 03:39 AM   #16
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Hi Dan et al

I can likely help as well, but a couple things:
The classification definitely makes sense, but I reckon it would also be helpful to have everything in one table so it can be copied out.

Also some of the genomes are really -well sequenced- but far from being assembled in any useful way.
So potentially one would not even only include a quality column but potentially even N50 if assembled?
(And would this reflect only published genomes? We have Solanum pennellii assembled to an N50 of above 1Mbase, also the beta vulgaris genome is pretty complete)

I would probably do the Solanacae and can provide some insight there.

Cheers,
björn
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Old 07-10-2013, 05:42 AM   #17
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The original intention of the page was 'public and published', but I've relaxed it a bit to include some currently unpublished genomes (annotated with the year "2013?") and even a couple where the assembly isn't even public yet (private communication)...

You're right, we should annotate this clearly. At the very least I'm planning to add an 'ENA/BioProject' column with links to genome assemblies / bioprojects to make it absolutely clear when the assembly is public property.

Adding assembly methods and statistics (and version) would be great too...

About building one big table... Can we just cram the headers into the table design? Or should we have multiple classification columns? Whatever works I guess?

I'm starting to get 'not-on-my-wiki' syndrome and feel the desire to pull this into SEQwiki for ultimate control, but having it on WP is the most visible, and will hopefully keep the page most up to date. Later we can publish it as a review in PLoS ;-)

Cheers,
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Old 07-10-2013, 05:45 AM   #18
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Also... anyone good with WikiData? We could put all figures in there:
http://www.wikidata.org/wiki/Wikidat...ogy_task_force
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Old 07-10-2013, 11:13 AM   #19
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Quote:
Originally Posted by dan View Post
I'm starting to get 'not-on-my-wiki' syndrome and feel the desire to pull this into SEQwiki for ultimate control, but having it on WP is the most visible, and will hopefully keep the page most up to date. Later we can publish it as a review in PLoS ;-)
How about adapting the SEQanswers/SEQwiki model by linking comments and discussion on the WP data back to SEQanswers forum?
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Old 07-10-2013, 12:09 PM   #20
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Absolutely. I'll populate some info tonight
Column added... Fire away my friend!
http://en.wikipedia.org/wiki/List_of..._plant_genomes
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