There appear to be genomes available. See:

https://ddbj.nig.ac.jp/DRASearch/query?organism=Panicum%20virgatum

It seems I should do a De novo asembly on the whole genome reads and then I use it as a reference genome for alignment.

Is there any .fastq format file of Panicum Virgatum genome?

What about GFF (General Feature Format) file?

You can download the raw reads in Fastq format here:

https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Panvirsequencing_103_FD

Kandasamy Ulaganathan

Thanks Dr. Ulaganathan

But .fastq file is a collection of short reads.

how can I use it for my RNA-Seq reads. I need a .fa file to align the RNA-Seq reads to the genome.

Dear Razavi

You can do a De novo assembly of the reads and use the transcripts for your further work

Sincerely

K.ULAGANATHAN

If you ever want to do RNAseq work but have no reference things like Trinity are your friend.

https://github.com/trinityrnaseq/trinityrnaseq/wiki

An alternative might be to use a reference genome from another species from the same family. Based on the NCBI Genome database, there are two species in the same family with reference genomes, i.e., P. miliaceum and P. hallii. P. miliaceum seems to have a better genome assembly as a better known crop. You might want to try use that to see whether it works.

https://www.ncbi.nlm.nih.gov/genome/44156

Dear Xinkun Wang and Kandasamy Ulaganathan .

There are reference genome and gff annotation files of Panicum Virgatum (Switchgrass), in this link:

https://genomevolution.org/coge//GenomeInfo.pl?gid=25460

Also the list of all Panicum available in this link:

https://genomevolution.org/coge//SearchResults.pl?s=panicum

https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvirgatum