## 2 Results
### Target Prediction of miRNAs in C. sativa
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**miRNA Name** & **Target ID** & **Target Annotation** & **Expectation** & **Pathway** \\ \hline CsmiRNA-n34g.2 & T\_00038493 & & 2.5 & \\ \hline CsmiRNA-n34a-5p & & & 0 & \\ CsmiRNA-n34b-5p & & & 0.5 & \\ CsmiRNA-n34d-5p & & & 1 & \\ CsmiRNA-n34d.1-5p & & & 2 & \\ CsmiRNA-n34d.2 & & DXS & 3 & \\ CsmiRNA-n34e-2.3p & T\_00064406 & & 0.5 & \\ CsmiRNA-n34e-2.5p & & & 0.5 & \\ CsmiRNA-n34f.1-5p & & & 3 \\ CsmiRNA-n34f.2-5p & & & 1.5 & \\ CsmiRNA-n34h.2-3p & & & 2.5 & \\ CsmiRNA-n57-5p & & & 1.5 & \\ \hline CsmiRNA-n28 & T\_00018927 & & 1.5 & \\ CsmiRNA-n28 & T\_00018928 & HDR & 1.5 & \\  & T\_00018929 & & 1.5 & \\ \hline miR56e-3p & T\_00090667 & & 3 & \\ \hline CsmiRNA-n34e4 & & LOX & 2.5 & \\ CsmiRNA-n33e-3p & T\_00023465 & & 2.5 & \\  & T\_00023466 & & 2.5 & \\ \hline CsmiRNA-n52a & & & 3 & \\ CsmiRNA-n52d & & & 3 & \\ CsmiRNA-n52d & T\_00067318 & & 3 & \\ CsmiRNA-n52f & & & 3 & \\ \hline CsmiRNA-n52a & & & 3 & \\ CsmiRNA-n52a & & & 3 & \\ CsmiRNA-n52a & T\_00067320 & & 3 & \\ CsmiRNA-n52f & & & 3 & \\ \hline miR530-3P & T\_00087904 & & 3 & \\ \hline CsmiRNA-n27a.2 & & & 1 & \\ CsmiRNA-n27c.2 & & & 2.5 & \\ CsmiRNA-n27d-3p & & & 2 & \\ CsmiRNA-n27e-3p & & & 2 & \\ CsmiRNA-n27f & T\_00016027 & & 1.5 & \\ CsmiRNA-n27g-3p & & & 0.5 & \\ CsmiRNA-n27f & & & 0.5 & \\ CsmiRNA-n27n-3p & & & 0.5 & \\ \hline CsmiRNA-n27a.1 & & & 2.5 & \\ CsmiRNA-n27b & & & 0 & \\ CsmiRNA-n27c.1 & & & 0.5 & \\ CsmiRNA-n27d-5p & & & 1 & \\ CsmiRNA-n27e-5p & & & 0 & cellulose \\ CsmiRNA-n27g-5p & & & 2.5 & \\ CsmiRNA-n27h & T\_00016031 & & 3 & \\ CsmiRNA-n27i-5p & & & 2.5 & \\ CsmiRNA-n27j & & & 1.5 & \\ CsmiRNA-n27f & & & 1.5 & \\ CsmiRNA-n27m & & & 1.5 & \\ CsmiRNA-n27m-5p & & & 1.5 & \\ CsmiRNA-n27g & & & 1.5 & \\ CsmiRNA-n27g & & & 1 & \\ CsmiRNA-n27p & & & 2 & \\ \hline CsmiRNA-n56b.1 & T\_00016799 & & 2 & \\ \hline miR5569b & & & 3 & \\ CsmiRNA-n1a-5P & T\_00035890 & & 3 & \\ \hline miR5569b & & & 3 & \\ CsmiRNA-n1a-5P & T\_00035891 & & 3 & \\ \hline miR5569b & & & 3 & \\ CsmiRNA-n1a-5P & T\_00035890 & & 3 & \\ \hline miR5569b & & & 3 & \\ CsmiRNA-n1a-5P & T\_00035891 & & 3 & \\ \hline \hline \end{tabular}
\end{table} 
Table 1: _Cont._ \begin{table}
\begin{tabular}{c c c c} \hline
**miRNA Name** & **Target ID** & **Target Annotation** & **Expectation** & **Pathway** \\ \hline miR5569b & & 3 & \\ CsmiRNA-n1a-5P & T\_00035895 & 3 & \\ \hline CsmiRNA-n22c-5p & T\_00043674 & 3 & \\ \hline CsmiRNA-n22c-5p & T\_00043675 & 3 & \\ \hline CsmiRNA-n22c-5p & T\_00043676 & 3 & \\ \hline CsmiRNA-n22c-5p & T\_00043677 & 3 & \\ \hline CsmiRNA-n22c-1 & T\_00051204 & 3 & \\ \hline CsmiRNA-n37a-3p & T\_00068566 & 3 & \\ \hline CsmiRNA-n37a-3p & T\_00068567 & 3 & \\ \hline miR8569b & & 3 & \\ CsmiRNA-n1a-5P & T\_00078801 & 3 & \\ \hline miR8569b & & 3 & \\ CsmiRNA-n1a-5P & T\_00078803 & 3 & \\ \hline miR8569b & & 3 & \\ CsmiRNA-n1a-5P & T\_00078805 & 3 & \\ \hline  & T\_00080222 & 3 & \\ \hline  & T\_00080223 & 3 & \\ \hline  & T\_00080224 & 3 & \\ \hline  & T\_00087551 & 3 & \\ \hline  & T\_00087552 & 3 & \\ \hline  & T\_00087553 & 3 & \\ \hline  & T\_00087554 & 3 & \\ \hline  & T\_00087555 & 3 & \\ \hline  & T\_00087555 & 3 & \\ \hline  & T\_00087555 & 3 & \\ \hline  & T\_00087556 & 3 & \\ \hline  & T\_00087557 & 3 & \\ \hline  & T\_00087558 & 3 & \\ \hline  & T\_00087559 & 3 & \\ \hline  & T\_00087560 & 3 & \\ \hline miR8482a-3p & & 3 & \\ miR8482b-3p & T\_00093433 & 3 & \\ \hline miR82a-3p & & 3 & \\ \hline miR82b-3p & T\_00093434 & 3 & \\ \hline miR82c-3p & & 3 & \\ \hline miR8508-5p & T\_00012561 & 3 & \\ CsmiRNA-n34c-3p & T\_00012569 & 3 & \\ \hline  & T\_00054754 & VILIN & 3 \\ \hline \end{tabular}
\end{table} 
Table 1: _Cont._Subsequently, the crosstalk between AS and miRNAs involved in cannabinoids, FA and cellulose was analyzed. As shown in Table S12, there were two types for the miRNAs acting on the isoforms of the structural gene. One was miRNAs targeting all the isoforms of one structural gene. For example, CsmiRNA-n33j.1-3p targeted the transcripts (T_00033798/00033799/00033800) of AAE.