Table 3.
Intrusive growth-related down-regulated lus-miR families and their up-regulated target genes identified from the comparison of phloem fibers at the stages of intrusive elongation and cell wall thickening (a cutoff of comparison either iFIBa vs. tFIB, or iFIBb vs. tFIB has a log2FC value ≥2 or ≤−2 with padj < 0.05); FC; fold change.
| Family of miR | Member of lus-miR Family | Transcript ID | At Homolog | At Symbol | Description | iFIBa vs. tFIB, log2FC | padj | iFIBb vs. tFIB, log2FC | padj |
|---|---|---|---|---|---|---|---|---|---|
| miR156 | a | Lus10021034 | AT2G42200 | SPL9 | squamosa promoter binding protein-like 9 | 4.43 | 3.68 × 10−89 | 4.67 | 5.11 × 10−99 |
| a | Lus10002430 | AT3G62390 | TBL6 | TRICHOME BIREFRINGENCE-LIKE 6 | 3.34 | 8.55 × 10−12 | 3.12 | 2.46 × 10−10 | |
| a | Lus10023818 | AT2G42200 | SPL9 | squamosa promoter binding protein-like 9 | 2.87 | 1.04 × 10−10 | 2.85 | 1.60 × 10−10 | |
| a | Lus10024555 | AT4G12110 | SMO1 | sterol-4alpha-methyl oxidase 1-1 | 2.53 | 8.25 × 10−33 | 2.61 | 1.20 × 10−34 | |
| a | Lus10012020 | AT2G42200 | SPL9 | squamosa promoter binding protein-like 9 | 2.44 | 6.94 × 10−19 | 2.25 | 4.82 × 10−16 | |
| a | Lus10021141 | AT1G69170 | Squamosa promoter-binding protein-like (SBP domain) transcription factor family protein | 2.08 | 2.14 × 10−10 | 1.46 | 1.87 × 10−5 | ||
| a | Lus10007726 | AT3G49760 | bZIP5 | basic leucine-zipper 5 | 1.97 | 6.20 × 10−3 | 3.23 | 2.10 × 10−6 | |
| miR159 | a | Lus10027321 | AT5G47560 | TDT | tonoplast dicarboxylate transporter | 4.99 | 5.39 × 10−3 | 6.78 | 9.58 × 10−5 |
| a | Lus10031827 | AT5G12930 | 3.86 | 1.89 × 10−19 | 3.31 | 2.65 × 10−14 | |||
| a | Lus10041729 | AT5G25620 | YUC6 | Flavin-binding monooxygenase family protein | 3.8 | 2.85 × 10−2 | 4.62 | 6.86 × 10−3 | |
| a | Lus10016550 | AT5G07900 | Mitochondrial transcription termination factor family protein | 3.23 | 1.81 × 10−7 | 2.77 | 1.38 × 10−5 | ||
| a | Lus10034196 | AT3G11920 | glutaredoxin-related | 3.06 | 1.60 × 10−8 | 2.18 | 1.17 × 10−4 | ||
| a | Lus10031256 | AT5G12930 | 3.04 | 2.98 × 10−6 | 2.61 | 1.02 × 10−4 | |||
| a | Lus10019870 | AT3G19184 | AP2/B3-like transcriptional factor family protein | 2.11 | 5.70 × 10−4 | 1.43 | 3.14 × 10−2 | ||
| miR166 | a,b,c,d,e,f,g,h,i,j,k | Lus10029117 | AT1G17100 | SOUL hem × 10-binding family protein | 7.05 | 6.17 × 10−5 | 6.78 | 1.43 × 10−4 | |
| b | Lus10022678 | AT3G51740 | IMK2 | inflorescence meristem receptor-like kinase 2 | 3.04 | 3.50 × 10−12 | 2.87 | 8.73 × 10−11 | |
| a,c,d,e,f,g,h,i,j,k | Lus10030381 | AT2G45850 | AT hook motif DNA-binding family protein | 2.87 | 4.96 × 10−33 | 2.56 | 4.37 × 10−26 | ||
| a,b,c,d,e,f,g,h,i,j,k | Lus10027060 | AT3G59680 | 2.67 | 4.26 × 10−4 | 3.39 | 4.96 × 10−6 | |||
| a,b,c,d,e,f,g,h,i,j,k | Lus10023357 | AT2G34710 | HB14,PHB | Homeobox-leucine zipper family protein/lipid-binding START domain-containing protein | 2.42 | 1.15 × 10−39 | 2.13 | 8.75 × 10−31 | |
| a,b,c,d,e,f,g,h,i,j,k | Lus10037568 | AT1G52150 | HB15,CNA,ICU4 | Homeobox-leucine zipper family protein/lipid-binding START domain-containing protein | 2.38 | 8.48 × 10−55 | 2.01 | 7.92 × 10−39 | |
| a,b,c,d,e,f,g,h,i,j,k | Lus10038449 | AT2G34710 | HB14,PHB | Homeobox-leucine zipper family protein/lipid-binding START domain-containing protein | 2.3 | 3.80 × 10−39 | 2.09 | 4.33 × 10−32 | |
| a,c,d,e,f,g,h,i,j,k | Lus10037696 | AT5G63950 | CHR24 | chromatin remodeling 24 | 2.21 | 2.98 × 10−20 | 1.9 | 4.84 × 10−15 | |
| a,b,c,d,e,f,g,h,i,j,k | Lus10011426 | AT4G32880 | HB8 | homeobox gene 8 | 2.13 | 1.14 × 10−32 | 1.79 | 4.14 × 10−23 | |
| a,b,c,d,e,f,g,h,i,j,k | Lus10011616 | AT4G32880 | HB8 | homeobox gene 8 | 2.1 | 5.98 × 10−14 | 1.94 | 5.89 × 10−12 | |
| a,b,c,d,e,f,g,h,i,j,k | Lus10025223 | AT3G56370 | Leucine-rich repeat protein kinase family protein | 2 | 1.31 × 10−18 | 2.1 | 3.33 × 10−20 | ||
| miR166 miR396 | b a,b,c,e |
Lus10012048 | AT3G19050 | POK2 | phragmoplast orienting kinesin 2 | 2.49 | 1.92 × 10−30 | 2.48 | 4.58 × 10−30 |
| miR167 | i | Lus10026283 | AT2G21180 | 4.41 | 4.80 × 10−2 | 4.7 | 3.59 × 10−2 | ||
| i | Lus10006347 | AT5G12080 | MSL10 | mechanosensitive channel of small conductance-like 10 | 2.68 | 6.14 × 10−4 | 2.8 | 3.62 × 10−4 | |
| i | Lus10029912 | AT3G05330 | ATTAN | cyclin family | 2.28 | 4.39 × 10−10 | 2.46 | 1.62 × 10−11 | |
| i | Lus10020804 | AT5G37020 | ARF8 | auxin response factor 8 | 2.19 | 1.21 × 10−20 | 1.98 | 5.94 × 10−17 | |
| i | Lus10038019 | AT2G46980 | 2.07 | 8.42 × 10−6 | 2.26 | 1.10 × 10−6 | |||
| i | Lus10031354 | AT5G37020 | ARF8 | auxin response factor 8 | 1.96 | 8.84 × 10−53 | 2.02 | 8.09 × 10−56 | |
| i | Lus10002960 | AT5G12080 | MSL10 | mechanosensitive channel of small conductance-like 10 | 0.88 | 4.13 × 10−1 | 2.03 | 3.15 × 10−2 | |
| miR319 | a | Lus10041994 | AT5G52450 | MATE efflux family protein | 2.9 | 2.27 × 10−25 | 2.26 | 1.44 × 10−15 | |
| a | Lus10004295 | AT5G49160 | DMT1,MET1,MET2 | methyltransferase 1 | 2.04 | 5.75 × 10−22 | 1.99 | 8.43 × 10−21 | |
| miR396 | a,b,c,e | Lus10038002 | AT2G45480 | GRF9 | growth-regulating factor 9 | 7.09 | 7.27 × 10−4 | 4.46 | 5.41 × 10−2 |
| a,b,c,e | Lus10019275 | AT2G22840 | GRF1 | growth-regulating factor 1 | 5.84 | 2.41 × 10−12 | 3.53 | 4.90 × 10−5 | |
| a,b,c,e | Lus10019274 | AT2G22840 | GRF1 | growth-regulating factor 1 | 5.14 | 1.60 × 10−23 | 2.78 | 2.52 × 10−7 | |
| a,b,c,e | Lus10000473 | AT3G13960 | GRF5 | growth-regulating factor 5 | 4.75 | 6.53 × 10−5 | 3.55 | 4.21 × 10−3 | |
| a,b,c,e | Lus10011559 | AT2G22840 | GRF1 | growth-regulating factor 1 | 4.5 | 2.91 × 10−6 | 2.11 | 4.80 × 10−2 | |
| a,b,c,e | Lus10009234 | AT2G45480 | GRF9 | growth-regulating factor 9 | 4.06 | 2.83 × 10−2 | 3.6 | 6.19 × 10−2 | |
| a,c | Lus10042952 | AT1G18370 | HIK,NACK1 | ATP binding microtubule motor family protein | 3.49 | 9.07 × 10−39 | 3.32 | 7.30 × 10−35 | |
| a,b,c,e | Lus10011558 | AT2G22840 | GRF1 | growth-regulating factor 1 | 3.48 | 4.32 × 10−12 | 0.67 | 2.90 × 10−1 | |
| a,b,c,e | Lus10031717 | AT5G62360 | Plant invertase/pectin methylesterase inhibitor superfamily protein | 3.46 | 8.90 × 10−34 | 3.68 | 4.89 × 10−38 | ||
| a,c | Lus10032452 | AT1G18370 | HIK,NACK1 | ATP binding microtubule motor family protein | 3.19 | 3.52 × 10−41 | 3.17 | 1.55 × 10−40 | |
| a,b,c,e | Lus10028754 | AT1G64080 | 3.04 | 6.45 × 10−6 | 0.82 | 3.35 × 10−1 | |||
| a,c | Lus10004012 | AT3G61740 | ATX3,SDG14 | SET domain protein 14 | 2.9 | 2.28 × 10−7 | 3.22 | 7.72 × 10−9 | |
| d | Lus10024639 | AT4G23440 | Disease resistance protein (TIR-NBS class) | 2.76 | 2.89 × 10−4 | 1.62 | 5.34 × 10−2 | ||
| d | Lus10039159 | AT1G33500 | 2.71 | 3.25 × 10−2 | 2.57 | 4.91 × 10−2 | |||
| a,b,c,e | Lus10010519 | AT3G06030 | MAPKKK12,NP3 | NPK1-related protein kinase 3 | 2.69 | 9.82 × 10−26 | 2.61 | 4.96 × 10−24 | |
| b,e | Lus10006983 | AT5G57655 | xylose isomerase family protein | 2.59 | 1.22 × 10−42 | 2.01 | 7.05 × 10−26 | ||
| a,b,c,e | Lus10027933 | AT3G19050 | POK2 | phragmoplast orienting kinesin 2 | 2.57 | 2.29 × 10−32 | 2.61 | 3.04 × 10−33 | |
| d | Lus10018093 | AT3G48210 | 2.47 | 1.92 × 10−19 | 2.38 | 5.86 × 10−18 | |||
| a,b,c,e | Lus10033441 | AT3G13960 | GRF5 | growth-regulating factor 5 | 2.46 | 7.44 × 10−5 | 1.56 | 1.92 × 10−2 | |
| a,b,c,e | Lus10033236 | AT4G24150 | GRF8 | growth-regulating factor 8 | 2.25 | 8.03 × 10−4 | 1.1 | 1.56 × 10−1 | |
| a,b,c,e | Lus10008268 | AT4G24150 | GRF8 | growth-regulating factor 8 | 2.24 | 1.04 × 10−3 | 1.05 | 1.80 × 10−1 | |
| a,b,c,e | Lus10009533 | AT3G13960 | GRF5 | growth-regulating factor 5 | 2.21 | 2.19 × 10−14 | 1.23 | 7.23 × 10−5 | |
| b,e | Lus10043134 | AT1G04730 | CTF18 | P-loop containing nucleoside triphosphate hydrolases superfamily protein | 2.15 | 9.94 × 10−21 | 2.2 | 1.37 × 10−21 | |
| d | Lus10004364 | AT4G16820 | PLA-I{beta]2 | alpha/beta-Hydrolases superfamily protein | 2.12 | 3.86 × 10−15 | 1.28 | 7.12 × 10−6 | |
| a,c | Lus10037136 | AT1G69440 | AGO7,ZIP | Argonaute family protein | 2.1 | 1.60 × 10−10 | 0.27 | 5.49 × 10−1 | |
| d | Lus10034335 | AT1G25400 | 1.75 | 1.72 × 10−4 | 2.09 | 5.30 × 10−6 |