Fig. 4
From: Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome
Experimentally confirm SNPs-causing 9930-unique target Csa5M146230.1. a. 9930-unique target Csa5M146230.1 for miRNA159c confirmed by degradome sequencing. The base pair of miRNA159c with Csa5M124230.1 and the base pair of Csa5M124230.1 with its orthologous hardwickii gene evm.model.Chr5.394 were showed on the top. The red vertical two points represent match base pair and one red vertical dot representing a G-U pair between miR159c and Csa5M124230.1. The black vertical bars represent the same base between Csa5M124230.1 and evm.model.Chr5.394. The black circle represents a SNP. The degradome sequencing data is plotted on the bottom. The left plot represents degradome tags distributing on mRNA of Csa5M124230.1(black dots), and the red dot represents the most abundant cleavage tag derived from mRNA cleavage site according to related statistical analysis of Cleaveland 2.0 software. The right plot represents degradome tags distributing on mRNA of evm.model.Chr5.394, and no statistical significant cleavage site can be detected. b. Real-time PCR analysis for Csa5M124230.1 (black columns) and evm.model.Chr5.394 (red columns) in roots, stems and leaves of 9930 and hardwickii, respectively. SE bar are shown. The y-axis representing relative expression compared to 9930 roots. c. Diagrammatic representation of Csa5M124230.1 cleavage sites are showed on the top. Thick black line represents mRNA of Csa5M124230.1. The putative miRNA interaction site is shown as a white box, with the nucleotide position within mRNA indicated. The miRNA sequence and partial sequence of Csa5M124230.1 are shown in the expanded regions. Horizontal arrowhead indicates gene-specific primer sites used for 5’ RACE. On the bottom, ethidium bromide-stained agarose gel showing the 5’RACE for six selected 9930-unique targets (1: Csa5M124230.1;2:Csa6M040600.1;3:Csa4M016490.1;4:Csa1M029600.1; 5: Csa6M423430.1; 6: Csa4M290150.1) listed in the additional file 9, and the number one corresponding to 5’ RACE reactions specific for Csa5M124230.1. Lane M, 2 k-plus ladders