Table 1. Differences between de novo generated and conserved miRNA genes in O. sativa and A. thaliana.
| O. sativa | A. thaliana | |||||
| de novo | Conserved | P-valuea | de novo | Conserved | P-value | |
| Adenine at first nucleotide | 39.29% | 5.13% | <10−3 | 13.04% | 5.48% | <10−3 |
| miRNA length (nt) | 22.37 | 21.00 | <10−3 | 21.74 | 20.91 | <10−3 |
| Precursor length (nt) | 171.85 | 119.17 | <10−3 | 196.32 | 140.01 | 0.001 |
| Stem length (nt) | 83.95 | 57.42 | <10−3 | 96.71 | 68.04 | 0.001 |
| Distance between miR and loop(nt) | 43.27 | 22.78 | <10−3 | 41.16 | 22.10 | 0.001 |
| Loop length (nt) | 5.95 | 6.33 | 0.176 | 4.90 | 5.93 | 0.113 |
| Match ratio of hairpinb | 80.03% | 74.34 | <10−3 | 75.52% | 72.85% | 0.097 |
| siRNA (#)c | 1.50 | 0.40 | <10−3 | 4.11 | 1.38 | <10−3 |
| Multi-miRNAd | 6.08% | 0.00% | 0.008 | 21.05% | 0.00% | <10−3 |
| Locatione | 34.81% | 7.76% | <10−3 | 15.79% | 6.94% | 0.266 |
| Promoter (#)f | 0.52 | 1.29 | / | 0.58 | 1.35 | / |
| SSRs (#)g | 0.46 | 0.95 | <10−3 | 0.32 | 0.72 | 0.020 |
| Target number (#) | 20.69 | 8.53 | <10−3 | 10.90 | 8.25 | 0.244 |
| Target gene expression intensityh | 435.20 | 562.71 | 0.005 | 5.80 | 6.75 | 0.005 |
| Base pairings of cleaving sitei | 1.63 | 1.80 | <10−3 | 1.56 | 1.82 | <10−3 |
| Family size (#) | 5.53 | 13.46 | <10−3 | 1.53 | 6.12 | <10−3 |
| Conservationj | 1.23 | 8.70 | <10−3 | 1.58 | 8.04 | <10−3 |
| miRNA expression intensityk | / | / | / | 7.58 | 41.68 | 0.106 |
| Polymorphic site density of pre-miRNAl | / | / | / | 4.41% | 1.50% | 0.002 |
| Polymorphic site density of miRNA | / | / | / | 0.35% | 0.23% | 0.715 |
| Polymorphic site density of target | / | / | / | 4.44% | 2.46% | 0.118 |
| Methylcytosine densitym | / | / | / | 2.74% | 0.09% | <10−3 |
| Promotor methylcytosine densityn | / | / | / | 1.08% | 0.09% | <10−3 |
t-test.
Number of pairing bases/hairpin length.
Number of siRNAs encoded by miRNA precursor.
Percentage of miRNA precursor encoding more than one miRNA.
Percentage of miRNA genes located in coding gene regions.
Average promoter (TATA box) and enhancer number of a miRNA gene.
Simple sequence repeats number adjacent to miRNA gene within 1 kb region.
Mean of all gene expression intensity is 403.67 and 6.14 in O. sativa and A. thaliana respectively.
Watson-Crick pairing number of miRNA cleaving site (10 and 11 nucleotides) on miRNA/target duplex.
Orthologous number of miRNA gene in 14 plant species in miRbase.
miRNA expression data, polymorphism site data and DNA methylation data only have A. thaliana data.
Pre-miRNA polymorphic site number/pre-miRNA length. Polymorphic site density of the whole genome is 6.66%.
Pre-miRNA DNA methylation site number/pre-miRNA length. Methylcytosine density of the whole genome is 0.98%.
1 kb upstream of pre-miRNA DNA methylation site number/1000.