## 2 Results
### Cleavage Targets Guided by miRNAs  
miRNAs could act on their targets by cleavage [80]. In order to validate the authentic cleavage targets of miRNAs, a degradome library was sequenced, and psRobot software was used to analyze the cleavage site of target genes and the reads of degradation fragments [81]. As a result, a total of 10,810,702 clean reads represented by 5,623,324 unique sequences were obtained after high-quality filtering and removing the adapters and null inserts. Most of the miRNAs in plants target genes at the 9 th, 10 th and 11 th nucleotides of the complementary region between miRNA and mRNA, occasionally at the other site [82]. The cleavage sites of miRNA targets were predicted by psRobot software, as shown in Table S13. In total, 145 transcripts were identified, which were targeted by 62 miRNAs, including 40 conserved miRNAs and 22 C. _sativa_-specific miRNAs (Table S14). The major targets of conserved miRNAs were TFs involved in development, responding to abiotic stresses and metabolism. In aspects of development, for example, miR156 targeted 34 squamous promoter binding protein like transcripts (_SPLs_). In _Arabidopsis thaliana_ L. _SPLs_ played an important part in flowering development [83]. miR160 targeted six auxin response factor 16 (_ARF16_) transcripts. It was reported that miR160 regulated auxin mediated development by ARF10/16/17 in tomato through posttranscriptional regulation [84]. MiR164 targeted 10 CUP SHAPED COTYLEDON 2 (_CUC2_) transcripts. MiR164 regulated the axillary meristem formation by targeting _CUC1_ and _CUC2_, participating in the development of cotyledons and floral organs in _Arabidopsis_[85]. In response to abiotic stresses, 20 transcripts encoding NAC TFs were identified as targets of miR164. NAC TFs were validated for response to salinity as well as high temperature and drought stresses in _Brassica juncea_ L. [PERSON] [86]. In aspects of metabolism, miR393 targeted two transport inhibitor response 1 (_TIRI_) genes and two auxin signaling f-box 2 (_AFB2_) genes. In _Arabidopsis, TIR1_ and _AFB2_ had an effect on the auxin sensitivity [87]. In addition, 16 ubiquitin-conjugating E2 enzyme transcripts were targeted by miR399. A previous study showed that miR399 targeted ubiquitin-conjugating E2 enzyme genes functioning in the control of inorganic phosphate homeostasis in _Arabidopsis_[88]. A few _C. sativ_-specific miRNAs were also found, including CsmiRNA-n56/n10/n27/n30 and other proteins. For catalysis, CsmiRNA-n56 targeted two cytokinin hydroxylase (_CYP735A1_) genes. CYP735A1 is a cytochrome P450 monooxygenase, and it was demon \begin{table}
\begin{tabular}{c c c c} \hline
**miRNA Name** & **Target ID** & **Target Annotation** & **Expectation** & **Pathway** \\ \hline miR172a-3p & & & 3 \\ CsmiRNA-n4b-5p & T\_00062735 & & 3 \\ \hline miR172a-3p & & & 3 \\ CsmiRNA-n4b-5p & & & 3 \\ \hline CsmiRNA-n24m.1 & T\_00064946 & CSL & 2 \\ \hline CsmiRNA-n32e.2 & T\_00019352 & & 2.5 \\ \hline miR171a-5p & & & UDP-galactose transporter & 3 \\ miR171b-5p & T\_00021321 & & 3 \\ \hline AAE: acyl-activating enzyme; DXR: 1-deoxy-D-xylulose 5-phosphate reductio isomerase; DXS: 1-deoxy-D-xylulose-5-phosphate synthase; HDR: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; LOX: lipoxygenase; ACCase: acetyl-CoA carboxylase; COBL: COBRA-like protein; CESA: Cellulose synthase; FRA: inositol polyphosphate 5-phosphatase; CSL: Cellulose synthase-like protein. \\ \hline \end{tabular}
\end{table} 
Table 1: \(Cont.\)strated that it catalyzed the biosynthesis of _trans_-Zeatin in _Arabidopsis_[89]. CsmiRNA-n10 targeted the 3-hydroxy-3-methylglutaryl-coenzyme A reductase gene, which catalyzed the HMG-CoA to form MVA [90]. CsmiRNA-n27 targeted the U-box domain-containing protein, which participated in the initial fruit developmental stage in _Musa acuminate_ L [91]. In addition, CsmiRNA-n30 targeted tubby-like F-box protein, which functioned in abiotic stress tolerance in _Manihot esculenta_ [PERSON] [92].