2.4 Functional annotation of transcriptome
Functional annotation was performed by using Trinotate pipeline v3.2.1
(http://trinotate.github.io), which
utilizes the homology search based on Swissprot, Pfam, and NCBI-BLAST-nr
(non-redundant) databases from the CD-hit clustered trinity transcript
IDs and TransDecoder derived peptide sequences. The cut-off E-value for
the BLAST search was adjusted between 1.0-5 and
1.0-100 and the homology search was performed with
default parameters. Additional tools, such as SignalP, tmHMM, and
RNAMMER (http://www.cbs.dtu.dk/services/), were integrated into
the Trinotate pipeline to determine probable signal peptides,
transmembrane helices, and residual rRNA transcripts, respectively, in
the assembled transcriptome. All the major transcription factor families
and transcriptional regulators were determined using the PlantTFcat tool
(http://plantgrn.noble.org/PlantTFcat/).