Which rice genome should I use for reference based transcriptome assembly of indica varieties of rice

Question

[sharadlko1]

I want to identify the polymorphic EST-SSRs and SNPs in three different indica varieties of rice for which I have got the RNA-Seq PE reads. In order to identify polymorphic EST-SSRs and SNPs, I plan to assemble the transcripts from each variety, using hisat2/stringtie2 pipeline. I have read several papers, where Nipponbare (a rice variety of japonica group) genome (MSU7/IRGSP1.0), has been used for reference based transcriptome assembly of indica varieties. In Ensemble, there is reference genome for indica and japonica variety. It is making me confused. Please advise me which reference genome should I use. Thanks.

[GenoMax]

In Ensemble, there is reference genome for indica and japonica variety.

If your rice is Indica then you should use that reference. You can find NCBI's genome version here. Transcript file is found on the same page.

Ensembl's genome build is found here. Transcript files are available here.

[sharadlko1]

I agree with you that I should use indica reference genome but I am wondering why in so many papers, authors used japonica reference genome to align the indica RNA-seq reads. You have also given me the link of transcripts of reference genome. May I use only transcripts (not the genome) to map my reads in order to assemble transcripts for downstream analysis of polymorphic EST-SSRs and SNPs. Please advise me.Thanks.