[BioC] How can reach a specific annotation of phytozome by using biomaRt library

[Mao Jianfeng]

Dear lister,

I am new to bioconductor and genomics, coming from classical
statistics using R. Now, I am working on population genomics of a
plant species Arabidopsis lyrata.

I would like to using biomaRt library to get my genomic variant (snp,
indel, CNV) in VCF4.0 format annotated by the available
gene/protein/pathway annotations of Arabidopsis lyrata stored in
Pytozome (http://www.phytozome.net/search.php) by using biomaRt
package.

I have read the manual of biomaRt package. But, unfortunately, the
example of biomaRt is only for Human which is different to a plant.
Now, I lost my directions of using biomaRt package, for example how to
link to phytozome, how to choose the right dataset for annotation.

Could you please show me some lines of R code to let me start? I can
not reach any helps around me.

Looking forward to hearing from you. Thanks in advance.

the phytozome websit for annotation data of Arabidopsis lyrata:
ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v6.0/Alyrata/annotation/

-- 
Jian-Feng, Mao