Table 1. Target gene prediction of conserved and novel miRNAs showing differential expression in root and shoot.
| miRNA | Expect Value | Accession |
Annotation | |
|---|---|---|---|---|
| B. juncea | B. rapa | |||
| Targets for differentially induced conserved miRNA in root and shoot | ||||
| bra-miR158-3p | 2.5 | Brara.I01252.1 | PPR repeat containing protein | |
| bra-miR161-5p | 1.5 | c127222_g1_i1 | PPR repeat-containing protein | |
| bra-miR171e | 0 | TCONS_00042811 | Scarecrow-like protein 6 | |
| bra-miR390-3p | 3 | Brara.H02653.1 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 18 HOMOLOG | |
| bra-miR403-3p | 2 | Brara.I05028.1 | YqaJ-like viral recombinase domain (YqaJ) | |
| bra-miR824 | 0.5 | Brara.K00360.1 | AGAMOUS-LIKE MADS-BOX PROTEIN AGL17-RELATED | |
| bra-miR157a | 1 | Brara.F03810.1 | SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN 10-RELATED | |
| bra-miR164a | 1 | TCONS_00044570 | NAC domain-containing protein 21/22 | |
| bra-miR172c-3p | 0.5 | TCONS_00050888 | AP2-like transcriptional factor | |
| bra-miR395-3p | 1.5 | c70764_g5_i1 | ATP sulfurylase | |
| bra-miR168b-5p | 3 | Brara.E01925.1 | EUKARYOTIC TRANSLATION INITIATION FACTOR 2 C | |
| bra-miR171a | 1 | TCONS_00056693 | Scarecrow-like protein 15 | |
| bra-miR172d-3p | 1 | TCONS_00012951 | AP2-like ethylene-responsive transcription factor TOE2 | |
| bra-miR390-5p | 2 | gi|674884630|emb|CDY47879.1| | Serine-type endopeptidase activity | |
| bra-miR396b-5p | 2 | TCONS_00046314 | Growth-regulating factor 1 | |
| bra-miR5654a | 2.5 | Brara.I05094.1 | PPR repeat family protein | |
| bra-miR1140 | 2.5 | Brara.I04295.1 | Pectate lyase superfamily protein | |
| bra-miR172b-5p | 3 | Brara.G00265.1 | ALUMINUM-ACTIVATED MALATE TRANSPORTER 4-RELATED | |
| bra-miR1885b | 0 | TCONS_00055693 | UDP-arabinose 4-epimerase | |
| bra-miR319-5p | 2 | TCONS_00058075 | Mechanosensitive ion channel domain-containing protein | |
| bra-miR395-5p | 1.5 | gi|656686826|gb| GBEQ01070429.1 | ATP sulfurylase | |
| bra-miR158-5p | 3 | Brara.C04365.1 | Arabidopsis protein of unknown function (DUF241) | |
| bra-miR161-3p | 2 | TCONS_00015119 | Pentatricopeptide repeat-containing protein | |
| bra-miR391-3p | 2 | TCONS_00063918 | Pentatricopeptide repeat-containing protein | |
| bra-miR396-3p | 2.5 | Brara.I02082.1 | PHOSPHATE TRANSPORTER PHO1 HOMOLOG 2-RELATED | |
| bra-miR9555a-3p | 3 | Brara.B01903.1 | Leucine-rich repeat transmembrane protein kinase | |
| bra-miR164a | 1 | TCONS_00044570 | NAC domain-containing protein 21/22 | |
| bra-miR395a-3p | 1.5 | c70764_g5_i1 | ATP sulfurylase | |
| bra-miR403-5p | 2.5 | Brara.I03870.1 | Plant protein of unknown function (DUF827) | |
| bra-miR5725 | 2 | c68837_g4_i12 | Kinase family protein | |
| bra-miR172d-5p | 3 | Brara.D00057.1 | Beta glucosidase 10 | |
| bra-miR160a-5p | 0.5 | c69810_g1_i2 | Auxin response factor 17-2 | |
| bra-miR161-3p | 2 | TCONS_00015119 | Pentatricopeptide repeat-containing protein | |
| bra-miR5712 | 1.5 | TCONS_00068909 | cDREB | |
| bra-miR9563a-5p | 2 | c60087_g2_i2 | Calmodulin-domain protein kinase CDPK isoform 2 | |
| Targets for differentially induced novel miRNA in root and shoot | ||||
| bra-miRX1 | 2 | Brara.H03095.1 | Fzo-like | |
| bra-miRX2 | 1.5 | Brara.D02054.1 | Pho2 | |
| bra-miRX3 | 2 | Brara.G00856.1 | Galactose Oxidase | |
| bra-miRX4 | 1.5 | Brara.B00890.1 | Brevis Radix-4 | |
| bra-miRX5 | 1.5 | Brara.K00675.1 | CBL-10 | |
The target genes for differentially induced conserved or novel miRNAs were predicted using transcriptome assembly of Brassica juncea or Brassica rapa genome (refer methodology for details regarding target prediction). The transcript sequences of all these targets used for primer designing are mentioned in Supplementary information-1.