Fig. 1

Expression analyses of tomato cysteine proteases reveal the involvement of SlVPE3 in fruit ripening. a Expression profiles of tomato cysteine protease genes during fruit ripening, as determined by quantitative RT-PCR. The ACTIN gene was used as the internal control. The stages of fruit development analyzed were mature green (MG), breaker (Br), orange (Or), and red ripe (RR). Expression ratios were calculated using the earliest stage (MG) as the denominator and plotted in a heat map on a log₂ scale. Each row in the color heat map represents a single cysteine protease gene. The green and red colors indicate down- and up-regulation, respectively, at an indicated ripening stage relative to the MG stage. Black indicates no significant expression change. Data from biologically repeated samples are averaged and the detailed information is listed in Additional file 2: Table S2. The genes whose mRNA levels increased more than tenfold are shown. b Gene identifiers (Solyc numbers) and functional annotations of the cysteine protease genes whose mRNA levels increased more than tenfold during tomato fruit ripening as revealed by quantitative RT-PCR. c Phylogenetic analysis of plant vacuolar proteases. The phylogenetic tree was produced using MEGA version 5.2. Bootstrap values from 1000 replications for each branch are shown. Tomato proteins are indicated in red. Species names are abbreviated as follows: St, Solanum tuberosum; Sl, S. lycopersicum; Nt, Nicotiana tabacum; Ca, Capsicum annuum; Gm, Glycine max; Cs, Citrus sinensis; Zm, Zea mays; At, Arabidopsis thaliana; Vv, Vitis vinifera; Os, Oryza sativa. The accession numbers are indicated in parentheses. d Gene expression of SlVPE3 in vegetative and reproductive tomato organs as determined by quantitative RT-PCR. The ACTIN gene was used as an internal control. Values are means ± standard deviation of three independent experiments