Transcriptomic analysis
Transcriptomic analysis was performed comparing the tillers that
flowered in the next season (17Hot) and tillers that remained vegetative
(17Control) as described in Samarth et al . (2019). 150 bp
generated paired-end reads were assembled into a single reference
transcriptome using the Trinity pipeline (Haas et al., 2013). Reads from
each of the samples were aligned to the reference assembly to generate a
count matrix using the Bowtie2.0 (Langmead & Salzberg, 2012) followed
by the differential expression analysis using the DESeq2 package in R.
The significantly differentially expressed genes (adj.
p-value<0.05) were annotated based on orthologous proteins
identified in B. distachyon using blastp with an E-value of
10-5 and 50% protein identity. Gene ontology and
pathway enrichment analysis was performed based on the PANTHER server
(Mi et al., 2016). Validation of the RNA-seq results was performed using
RT-qPCR with a random selection of four genes from the transcriptomic
data (Appendix S2).