Transcript reconstruction using Trinity (Grabherr et al. 2011; Haas et al. 2013) was carried using de novo and genome-guided methods. By the de novo method, RNA-seq reads were first assembled into unique sequences of transcripts (contigs) using the Inchworm module within Trinity. Contigs were clustered by the Chrysalis module, and corresponding De Bruijn graphs that represent the possible different isoforms were constructed. In the final step, De Bruijn graphs were processed by the Butterfly module to produce full-length transcripts. In the genome-guided method, RNA-seq reads were first aligned to the genome using GMAP (Wu and Watanabe 2005). Based on these aligned-read clusters, the Chrysalis and Butterfly modules were consecutively executed to produce the final reconstructed transcripts. Transcripts generated by these two methods were combined using the “Program to Assemble Spliced Alignments” (PASA) (Haas et al. 2003) pipeline to build a complete set of unique transcripts corresponding to gene models.