## 3 Discussion  
In this study, transcriptome, small RNA and degradome libraries of hemp 'Yunma No.1' were constructed and comprehensively analyzed. Compared with previous studies in _C. sativa_, three advancements were made. Firstly, the protein-coding genes related to cannabinoids, FA and cellulose were mined, and the transporter and regulatory protein genes were systematically predicted. Secondly, to reveal the gene expression and regulation at post-transcriptional level, the AS, miRNAs and lncRNAs in _C. sativa_ firstly were predicted. A total of 27,907 AS events in _C. sativa_ were identified, and five AS events were validated by RT-PCR at random. Among them, AS occurred in some structural genes of the cannabinoids, FA and cellulose biosynthetic pathway. MiRNAs and lncRNAs functioned in multiple pathways. We focused on the top five KEGG enrichment pathways of miRNA/lncRNA targets. For miRNAs, it was reported that miR-362 targeted RecQ-mediated genome instability protein 1 [94]. miR-125b targeted ER alpha-1, 2-mannosidase and played a critical role in maintaining protein homeostasis in the mammalian secretory pathway [95], while, KAS II, GPI ethanolamine phosphate transferase 3 subunit O and CCR4-NOT transcription complex subunit 4 potentially targeted by miRNAs were not reported. KAS II was involved in fatty acid elongation from 16:0-ACP to 18:0-ACP [96]. GPI ethanolamine phosphate transferase 3 subunit O functioned in GPI-anchor biosynthesis [97]. The top five KEGG enrichment pathways targeting lncRNAs have not been revealed to date. For example, 1,4-alpha-glucan branching enzyme played a significant role in the biosynthesis of branched polysaccharides, glycogen and amylopectin [98]. All these results indicate the important regulation of miRNAs and lncRNAs in _C. sativa_. MiRNAs and lncRNAs potentially regulate the biosynthesis of cannabinoids, FA and cellulose in two aspects. On the one hand, they directly target the structural genes (Tables 1 and 2, Figure 5). On the other hand, they targeted the structural gene related regulatory protein genes. Previously, we determined some GA- or isoflav-related TFs, TRs and PKs potentially targeted by miRNAs, indicting the significant roles of regulatory protein genes in metabolism [77; 99]. Based on the known biosynthetic pathways of cannabinoids, [PERSON] et al. successfully biosynthesized cannabinoids along with the unnatural analogues in yeast [100], but the different isoforms of structural genes, regulatory protein genes and non-coding RNAs were not considered. In this study, only a strand-specific  
Figure 5: QRT-PCR validation of expression profiles of lncRNA/structural gene pairs of lncRNA880/AAE (**A**), lncRNA682/kinesin-like protein (**B**) and lncRNA578/COBL (**C**). The average expression profile of every gene in the root was chosen as a control and set to 1. RNA-Seq library was constructed. In the future, more libraries should be sequenced, and co-expression analysis will be carried out between the interested structural genes and regulatory genes to screen out and validate highly relevant regulators and make full use of them. Additionally, the crosstalk between AS and miRNAs or lncRNAs in the biosynthesis of cannabinoids, FA and cellulose was studied for the first time in _C. sativa_ (Tables S12 and S18). AS could regulate miRNA and lncRNA-mediated gene regulation by producing mRNA isoforms, which contained miRNAs/non-coding RNAs target sites or not [101]. A previous study revealed that the 44 of 354 identified miRNA binding sites were affected by AS in _Arabidopsis_[42]. Some lncRNA genes also possessed introns, leading to the production of lncRNA isoforms [102]. In _Arabidopsis_, [PERSON] et al. identified 135 cold-responsive lncRNAs, of which AS occurred in one-third [103]. In this research, the crosstalk between 17 lncRNAs and their target transcripts was predicted in _C. sativa_ (Table S18). During our work, a PacBio SMRT and a nanopore-based assembly genome of _C.