Sequence read mapping and assembly

The original image data produced by sequencing were transferred into sequences (raw reads). The calculating methods for raw reads was conducted according to Cock (2010). To obtain clean reads for further analysis, the raw reads were filtered by removing adaptor sequences, low-quality reads and reads with a percentage of unknown bases (N) of more than 10%. Following this, we used Bowtie to remove the ribosome reads (Langmead et al. 2009). The clean reads were mapped to the cucumber genome assembly (Chinese long) v2 (http://www.icugi.org/cgi-bin/ICuGI/index.cgi) according to Kim et al. (2013) and Trapnell et al. (2012).