Fig. 5

Global alternative splicing analysis of wild-type and AtSOAR1-transgenic plants under salt stress. A Statistics of different kinds of alternative splicing (AS) events in wild-type and OE-1 under normal and salt stress conditions. B Statistics of genes corresponding to different kinds of AS events. The red, blue, green and grey bars indicate salt-treated OE-1, salt-treated WT, OE-1 without treatment and WT without treatment, respectively, in (A) and (B). C Representative differential alternative splicing between WT and WT-S, or WT-S and OE-S were validated by RT–PCR and showed by IGV browser. The retained intron regions were marked by red box. Hydroponic cultured two-week-old seedlings were treated with 0 or 140 mM NaCl for 2 d followed by RNA extraction and cDNA synthesis. WT, wild-type plants without NaCl treatment; WT-S, wild-type plants with NaCl treatment; OE, AtSOAR1-transgenic plants OE-1 without NaCl treatment; OE-S, AtSOAR1-transgenic plants OE-1 with NaCl treatment. Actin 1 was taken as control for RT-PCR. D Frequency distribution of nucleotides around the splicing sites. The nucleotide sequences represent the consensus sequences of 5′- and 3′- splicing sites and the size of the letter indicates frequency of certain nucleotide. WT, WT-S and OE-S means nucleotides distribution around the splicing sites in wild-type, salt-treated wild-type and salt-treated OE-1 plants. WT-S/WT means nucleotides distribution around the splicing sites of salt-induced splicing events in wild-type. OE-S/WT-S means nucleotides distribution around the splicing sites of the new salt-induced splicing events in OE-1 compared with that of wild-type plants. Red boxes marked the altered frequency of the dominant A at position − 1 of 3′ splicing sites or the frequency of the C and G at position − 1 of the 5′ splicing sites