Table 3. DEGs across all libraries.

	L1:L2	L1:L3	L2:L3	L3:L4	L1:L4	L2:L4
Total	1714	4339	4013	2344	2115	1667
Up-regulated	759	2052	2157	1429	1069	1059
Down-regulated	955	2287	1856	915	1046	608

All the genes mapped to the reference sequence and genome sequences were examined for their expression differences across different libraries. Numbers of differentially expressed genes represent transcripts, using threshold values FDR≤0.001 and |log2 Ratio|≥1 for controlling false discovery rates. L1, L2, L3, and L4 represent the samples which were collected at stolon stage, initial swelling stage, middle swelling stage, and later swelling stage of rhizome, respectively.