Where Can I Download Latest Chromosome Sequences Of Oryza Sativa Indica Group?

Question

[Biomonika (Noolean)]

Hi all,

I have had really tough times trying to find actual version of oryza sativa indica chromosome sequences. Either I found something outdated with proper labeling of indica group or I find new assembly with no label, such as for example this:

ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Osativa/assembly/

so I have no idea whether it is actually japonica or indica..

Thank you very much for suggestions:) My second questions is about positions of centromeres. I have positions of those in japonica group. What do you think, how much are they going to differ?

Thanks.

[Biomonika (Noolean)]

I dont want to ask a new question, so.. is it just me or is it really difficult to find positions of Arabidopsis thaliana centromeres? I have found many browsers, but none with this track:(

Answer 1

[SES]

The assembly at Phytozome is from Nipponbare (a strain of subspecies japonica), and it is commonly used as the rice reference. You can find the indica assembly at Ensembl. You will also find some really useful information and data at the Gramene site. For investigating the positions of centromeres, explore the genome browsers for indica and japonica at Ensembl and Phytozome, respectively.

[Biomonika (Noolean)]

Thanks. Based on this discussion, I decided to switch to Nipponbare, as it may be easier to analyse.

Answer 2

[Vikas Bansal]

Look here. You can get japonica and indica both.

I think this one is latest.

[SES]

Note that indica and japonica are considered subspecies of O. sativa and are phenotypically distinct (indica is long-grain rice, japonica is short-grain rice). The cultivated line (I used the term strain before, but cultivar or line is more common) Nipponbare of subsp. japonica was chosen by the International Rice Genome Sequencing Project to serve as the reference. The difference between these assemblies is not a matter of versioning (hg18 vs. hg19), but these are distinct subspecies and you should the appropriate one for your study (use Nipponbare if you only need one "rice" genome).

[Biomonika (Noolean)]

Thanks. This is from 2006, I hoped for something newer.

[Vikas Bansal]

See my edit. May be that is the latest one.

[Biomonika (Noolean)]

This looks very good, but isnt Nipponbare a strain of subspecies japonica, as SES wrote?

[Vikas Bansal]

I am not so familiar with rice genomes, but the website says (according to SES also), it is commonly used as the rice reference. As in humans, there is hg18, hg19 etc commonly used as reference genome.

[Biomonika (Noolean)]

Thanks for help. I decided to analyse Nipponbare instead of Indica, because as you write, it is often used as reference.