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Table S1. Real-time RT-PCR primers used in the validation of novel miRNA expression. This pair of primer will amplify a photoreceptor gene (Unigene 35872) of Taxus mairei if total RNA is used as the template. In this study, small RNA was used as the PCR template, thus the amplification of Unigene 35872 was used as the negative control and cannot be used as the reference in the relative quantification of miRNA expression.

Table S2. Data cleaning in the degradome analysis. Total reads, total sequenced reads must be greater than 5 M; High quality, number of high quality reads without N, without more than four bases with quality score lower than 10 and without more than six bases with quality score lower than 13; 3′ adaptor null, number of reads without 3′ adaptor; insert null, number of reads without insert; 5′ adaptor contaminants, number of 5′ contaminants; smaller than 18 nt, number of reads less than 18 nt; small RNA tags are between 18 and 30 nts. Clean reads, number of clean reads used in the following analysis must be greater than 3 M.

Table S3. Small RNAs of Taxus mairei similar to miRNAs deposited in miRBase. Alignment score = match no. × 2 − mismatch no. − gap no. × 3.

Table S4. Family analysis of known miRNA. The occurrence of known miRNA families in Taxus mairei and other species is shown. For inter-specific comparison, miRNAs that are only found in Taxus (tmp) and belong to the known miRNA families are listed in the table; +, the miRNA family exists in the species; −, the miRNA family is absent in the species.

Table S5. Novel miRNAs and their targets predicted in Taxus. Id, name of the candidate novel miRNA; FES: fosmid end sequence of Taxus mairei genomic library (Hao et al. , ); minimal free energy should be less than −18 kcal mol−1; sequence (5p), candidate miRNA derived from 5′ part of the precursor; sequence (3p), candidate miRNA derived from 3 part of the precursor; UTR, untranslated region.

Fig. S1. Summary of the small RNA-sequencing experiment.

Fig. S2. Bioinformatic analysis of miRNA.

Fig. S3. Schematic depiction of degradome-sequencing library construction.

Fig. S4. Bioinformatic analysis of degradome.

Fig. S5. Stem loop structure of six candidate novel miRNAs predicted by Mfold.

Fig. S6. Base editing of Taxus miRNAs.

Appendix S1. Alignment between the candidate miRNA precursor and the derived 3′ and/or 5′ candidate novel miRNA predicted by Mireap.

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