Question: Where To Find The Genome Sizes Of Sequenced Plant Species?
7
gravatar for Zhaorong
10.0 years ago by
Zhaorong1.2k
State College, PA
Zhaorong1.2k wrote:

I thought this is a simple question, but after some searching over the Internet, I just found several out-of-date databases like http://data.kew.org/cvalues/

There are several useful resources though: http://www.phytozome.net/ http://www.plantgdb.org/ But I did not find any direct information on genome size.

A workaround would be to download all the fasta files of chromosome sequences of these species and just look at the file size..

I'm just wondering is there any resources on plant genome size, or if not, an efficient way to get this information?

Thank you!

genome plant • 6.5k views
ADD COMMENTlink modified 4.4 years ago by Antonio R. Franco4.4k • written 10.0 years ago by Zhaorong1.2k

It's important to stress that most eukaryotic genome size estimates are based on total DNA weight per cell. So, there plenty more estimates besides those in NCBI and related.

ADD REPLYlink written 9.2 years ago by Jarretinha3.3k
4
gravatar for Pierre Lindenbaum
10.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

From NCBI genome projects: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj

Clink on "Plant"

Each record contains the genome size (if available)

I would also suggest to have a the field gp:EstimatedGenomeSize/ in ftp://ftp.ncbi.nih.gov/genomes/genomeprj/gp.xml but it seems that not all the organisms are present in that file...

ADD COMMENTlink modified 7 months ago by RamRS26k • written 10.0 years ago by Pierre Lindenbaum127k
2
gravatar for Jarretinha
10.0 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

Hi Zhaorong,

Genome size or C-value as commonly used by biologists is a hard to find information. For instance, most biomolecular databases do not have this information readily available. NCBI has only a few hundred estimates on plant genomes. But, as of 2005 there are at least tens of thousands high quality estimates.

A good place is Plant C-value database in the Royal Botanic Gardens. But, be advised, I do not know database layout. So, it might not be possible to programmatically query the entries.

Anyway, for more information you can use T. Gregory 2004 book (The Evolution of the Genome) and check Michael Lynch's masterpiece (The Origins of Genome Architecture). Both bring a wealth of information on genome size, motif (TE, TFBS, etc.) contents, mutation rates, effective population size and other very useful estimates.

ADD COMMENTlink written 10.0 years ago by Jarretinha3.3k

I'll definitely read the books. Thank you :)

ADD REPLYlink written 10.0 years ago by Zhaorong1.2k
2
gravatar for Chris Miller
10.0 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

It's not comprehensive, but there are a few listed in the BioNumbers database

ADD COMMENTlink written 10.0 years ago by Chris Miller21k

Thank you for pointing it out! The bionumbers database is a cool idea.

ADD REPLYlink written 10.0 years ago by Zhaorong1.2k
1
gravatar for Darked89
10.0 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

You may try searching "Genome Projects" at NCBI with "txid33090[Organism:exp]" (green plants).

It is a crappy solution, since some entries seem to be duplicated, plastid/ chromosomal/ESTs projects are listed among WGS projects, but at least you should be able to extract info what is being sequenced and where. Individual genome centers/sequencing projects web pages may be the best one can get.

ADD COMMENTlink written 10.0 years ago by Darked894.2k

Thank you! This is what I end up with.

ADD REPLYlink written 10.0 years ago by Zhaorong1.2k
0
gravatar for Fred Fleche
10.0 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

Did you try to fill out the query form available at http://data.kew.org/cvalues/CvalServlet?querytype=1

It should allow you to get the statistics you are looking for

ADD COMMENTlink written 10.0 years ago by Fred Fleche4.3k
0
gravatar for Saeid Kadkhodaei
4.4 years ago by
IUT
Saeid Kadkhodaei90 wrote:

You may try:

http://www.ncbi.nlm.nih.gov/genome/

Then type your organism name, and it will direct you to the available genome information about your organism.

ADD COMMENTlink written 4.4 years ago by Saeid Kadkhodaei90
0
gravatar for Antonio R. Franco
4.4 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.4k wrote:

NCBI Mapviewer will provide you with many plant genomes with the inclusion of statistic, number of chromosomes, fasta files, genbank files, cross references to other useful databases and tools of interest, graphic maps and in some of them even more utilities such as specific Blast searches and so on

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Antonio R. Franco4.4k
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