Simultaneous measurement of rice and rice blast fungus transcripts in infected plants using RNA-seq provinfection-responsivensivexpressionon profiles for both rice and fungal transcripts.
A comparison showed that stage-enriched transcripts both in rice and Arabidopsis had similar distribution in most of functional terms but great difference in defence/stress response, signalling and transcription/RNA process.
Approximately 90 92% of rice and Arabidopsis transcript alignments met all of these strict validation criteria.
RPKM (Reads per kb per Million reads) was used to represent the gene expression level of rice and U. virens transcripts [ 48].
However, whole family-based expression analyses were carried out only in Arabidopsis, P. trichocarpa and rice, the transcript profiling of all family members is not available for the other plants.
Further, when we extended our comparisons with other sequenced grass genomes, we found that the Corvallis contigs hit 44,538 (∼67%) of 66,338 rice transcripts and 24,999 (∼84%) of 29,448 sorghum transcripts with similar results for the other two B. sylvaticum assemblies.
Data from our previous study of rice transcripts and other supportive studies in other species confirmed that our analysis captured the transcriptome for –P response in wheat.
Comparison of the down-regulated groups revealed similarities and differences, with the Abiotic Down group in rice and Arabidopsis, both showing enrichment of transcripts encoding kinases (5%vs.3%3% in the rice genome and 21% vs. 10% in the Arabidopsis genome).
We further aligned ASV1/ASV2 against currently-available non-rice transcripts and found that non-rice transcript evidence supported both ASV1 and ASV2 in Os08g0427300, Os01g0125900, and Os11g0661400, while non-rice evidence only supported ASV2 in Os05g0593300 and Os07g0648266 (Additional file 4).
Full length OsPYL9 primer was used and rice ubiquitin transcripts were used as control.
These yielded 422,960,068 transcripts from rice and 196,284,528 from Arabidopsis for further analysis.
