Table 1. Summary of Illumina transcriptome reads mapped to the reference genes (The numbers listed in the table are the sum of left and right reads).

Reads mapping	Reads number (%)
	Control-rep1 Control-rep2 Salt-stressed-rep1 Salt-stressed-rep2
Total reads	55051964	50888292	59933654	57599222
Total mapped reads	47295192(85.9%)	43513604(85.5%)	51183812(85.4%)	49765796(86.4%)
Unique match	44609343(81.03%)	40473327(79.53%)	47943836(79.99%)	43045674(74.73%)
Multi-position match	2685849(4.87%)	3040277(5.97%)	3239976(5.41%)	6720122(11.67%)
Total unmapped reads	7756772(14.1%)	7374688(14.5%)	8749842(14.6%)	7833426(13.6%)