Genomics and Applied Biology 2019, Vol.10, No.1, 1-9
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had 22 members, MIR395 had 14 members, MIR399 and MIR171_1 had 9 members, MIR166 and MIR156 had 8
members, MIR403 had 6 members, MIR160, MIR167_1 and MIR319 had 5 members, MIR396, MIR172 and
MIR164 had 4 members, MIR159, MIR398, MIR535 and MIR394 had 3 members, MIR393, MIR477 and
MIR482 had 2 members, MIR168, MIR390, MIR3630, MIR162_1, MIR408 and MIR397 had only 1 member
(Figure 2).
Table 2 Numbers of each small identified RNA classification
RNA types
Small RNA libraries
Bud
Second-leaf
Open surface leaf
Mature-leaf
Total of sRNA
5,403,620 (100.00%)
4,937,273 (100.00%) 6,242,272 (100.00%)
6,455,987 (100.00%)
Known_miRNA
95,439 (1.77%)
53,403 (1.08%)
144,779 (2.32%)
65,415 (1.01%)
rRNA
208,183 (3.85%)
85,117 (1.72%)
111,951 (1.79%)
29,153 (5.10%)
tRNA
1 (0.00%)
0 (0.00%)
0 (0.00%)
0 (0.00%)
snRNA
2,862 (0.05%)
2,025 (0.04%)
2,635 (0.04%)
4,785 (0.07%)
snoRNA
5,092 (0.09%)
1,209 (0.02%)
2,011 (0.03%)
4,591 (0.07%)
Novel miRNA
64,300 (1.19%)
53,835 (1.09%)
185,902 (2.98%)
71,123 (1.10%)
ta-siRNA TAS
25,231 (0.47%)
24,771 (0.50%)
43,484 (0.70%)
38,580 (0.60%)
Others
5,002,512 (92.58%)
4,716,913 (95.54%)
5,751,510 (92.14%)
5,942,340 (92.04%)
Figure 2 Members of miRNA family
Since tea plants do not have complete genomic sequencing data and do not have small RNA background, only the
unique small RNA sequences were mapped to the transcriptome of “Zijuan” tea tree to identify potential new
miRNA sequences. The symbolic hairpin structure of miRNA precursor was used in the prediction of new miRNA
(Friedlander et al., 2012; Wen et al., 2012). According to BLASTn search and the prediction of hairpin structure,
119 new mature miRNAs were found.
1.4 Prediction and functional analysis of miRNA target genes
The target genes of 126 known miRNA families and 119 new miRNAs were identified by psRobot software, and
the corresponding relationship between miRNA and target genes was obtained. The known miRNA families and
new miRNAs predicted 724 and 2,285 target genes, respectively, among which 207 and 678 were annotated to
function. These annotated target genes included transcription factors and functional gene families with different
biological functions. In this study, a single miRNA could regulate multiple target genes. For example, the known
miR156a had 27 target genes, while the new miRNA (novel_65) predicted 210 target genes. It was also predicted
that multiple miRNAs could regulate one target gene, and some of these miRNAs came from the same family and
some from different families.
