The differences in gene expression between −P and ++P stress in root and shoot (Supplementary Figure S7a, b) as well as the differences in gene expression between root and shoot under −P and ++P stress (Supplementary Figure S7c, d) suggest that Pi stress treatments have a significant effect on the overall expression profile of many genes involved in plant response to stress.
Interestingly, although the ratio of shoot-to-root weight clearly reversed between 10 and 15 days in the –P and ++P stress-treated plants, the weights of the plants decreased concordantly as reflected in differences in gene expression between the root and shoot (Supplementary Fig. S7).
Notably, the read count of tsRNAs was 2-fold greater in P-deficient shoots than in P-sufficient shoots (Supplementary Table S4).
The chloroplast-derived tsRNAs were the most abundant sRNA class, accounting for 22.7% of the total sRNAs in P-deficient shoots and 19% in P-sufficient shoots (Supplementary Table S7 under chloroplast sRNAs_tRNA).
Alignment of all the nuclear-derived reads to barley genes in the HVGI database identified 128 corresponding barley genes in P-sufficient shoots and 137 in P-deficient shoots (Supplementary Tables S5 under non-chloroplast sense sRNAs).
The two classes of sRNAs accounted for 80% of the mapped ncRNAs in P-deficient shoots and 76.3% in P-sufficient shoots (Supplementary Table S3).
tsRNAs derived from tRNA-Gly TCC) were tRNA-Gly TCCndant tsRNA species in both P treatments, accounting for 58.6% of the total tsRNAs in P-deficient shoots and 58.2% in P-sufficient shoots (Supplementary Table S4).
Seven hundred and ninety six and 715 ncRNAs were mapped in P-deficient and P-sufficient shoots, respectively, of which 114 ncRNAs were specific to P-deficient shoots, whereas 32 ncRNAs were specific to P-sufficient shoots (Supplementary Table S3).
A total of 1,336 –P responsive transcripts in the roots were not responsive to in the shoots (Supplementary Fig. S7c).
Of 683 shared ncRNAs, 176 were up-regulated whereas 51 were down-regulated in P-deficient shoots (Supplementary Table S3).
Six tsRNAs were significantly up-regulated (log2 > 1), whereas 4 were significantly down-regulated (log2 <–1), in P-deficient shoots (Supplementary Table S4).
