Figure 1.
Virus-free and ASGV-infected plantlets for RNA-Seq.
(A) ASGV-infected in vitro grown plantlets. (B) Detection of Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), Apple skin scar viroid (ASSVd) and Apple dimple fruit viroid (ADFVd) using RT-PCR with specific primers listed in Supplementary Table S1. ACTIN2 gene was used as an internal control. P, positive apple samples infected with ASGV, ACLSV, ASPV, ASSVd and ADFVd; H, healthy apple leaves. (C) Virus-free plantlets and Northern blotting to confirm ASGV elimination by thermotherapy. T11, T12, T25, T34, T35, T40, T45, T46, T47, T48, T55 and T60 represent regenerated apple plantlets after thermotherapy.
Figure 2.
Gene coverage statistics of the two RNA-seq libraries: virus-free and ASGV-infected.
Table 1.
Categorization and abundance of RNA-seq reads from libraries of virus-free and ASGV-infected apple shoots.
Figure 3.
Analysis of differentially expressed genes (DEGs) response to ASGV infection.
(A) Numbers of DEGs. (B) and (C) Distribution of fold changes (FC) for up-regulated and down-regulated DEGs, respectively.
Figure 4.
Function categorization of genes significantly induced (red) and repressed (green) in ASGV-infected apple plantlets.
Figure 5.
(A) Four up-regulated and four down-regulated DEGs randomly selected were confirmed by qRT-PCR. ACTIN2 gene was used as an internal control. Data are means and standard errors of three biological replicates. (B) Four DEGs randomly selected were confirmed by Northern blot. 18S RNA was used as a loading control.
Table 2.
A comparison of the results from RNA-seq and from qRT-PCR analyses of differentially expressed genes.
Figure 6.
Comparison of photosynthesis between virus-free and ASGV-infected apple shoots.
(A) Light response curves (net photosynthesis, Pn). (B) Intercellular CO2 concentration (Ci). (C) Stomatal conductance (gs). (D) Transpiration rate (Tr). Data represent means and standard errors based on measurements from six biological replicates. Asterisks indicate significant differences (P<0.05) between ASGV-infected and virus-free shoots under specific photo flux densities.