Removal of low quality reads

Sequence data

De novo assembly

Removal of sequences shorter than 1,000 bp

Blast against NCBI protein database

Removal of highly similar sequences (similarity > 90%)

Gene annotation

Analytical workflow ResultsSoftware

Back-mapping 50M reads to transcripts

ABySS-tofastqFASTX-toolkit

Velvet & Oases

CD-HIT

BLASTX

Blast2GO

Bowtie

Table 2

Gene expression profiles

Figs. 2a, b

Tables 3, 4, 5, 6 and S1; Fig. 1

Fig. S1