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.