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Table 2 Predicted R genes and the targeting miRNAs

From: Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves

Target Counts (RPKM) Annotation Predicted regulator miRNA
CK P
Onc 235 7.9 15.4 uncharacterized protein LOC100279616 miR2088, miR5654
Onc 649 12,.0 14.0 OsJNBa0083D01.14 miR1514
Onc 650 7.8 3.0 hypothetical protein OsI_07084 miR1510a*, miR1514
Onc 651 0 14.7 putative disease resistance protein I2 miR1514
Onc 1207 59.9 93.6 hypothetical protein OsI_15587 miR1510a*
Onc 1471 60.9 81.6 putative disease resistance protein RGA4 miR1514, miR5654
Onc 1537 86.2 85.7 hypothetical protein OsJ_14506 miR1514, miR2088, miR5654
Onc 1613 13.2 27.5 disease resistance protein I2 miR1510, miR529g
Onc 1615 28.1 15.7 NBS-containing resistance-like protein miR5246
Onc 1618 0.0 10.7 hypothetical protein OsI_07084 miR1510a*
Onc 1724 89.8 99.4 hypothetical protein SORBIDRAFT_08g020630 miR1514
Onc 2107 8.5 15.0 putative disease resistance protein miR156k, miR2088, miR5654
Onc 2524 18.5 27.2 putative disease resistance protein RGA2 miR2088
Onc 2555 24.6 60.0 putative disease resistance protein RGA4 miR1514
Onc 3695 11.7 22.9 CC-NBS-LRR R protein miR1510a*, miR529g
Onc 4069 36.1 32.0 hypothetical protein OsI_15587 miR1510a*, miR1514, miR2088, miR5246, miR5654
Onc 4126 0.0 17.4 CC-NBS-LRR R protein miR1510a*
Onc 4434 16.5 10.8 hypothetical protein VITISV_025836 miR2088, miR5654
Onc 4722 8.6 20.2 hypothetical protein OsI_07084 miR1510a*, miR894
Onc 4724 41.8 107.4 NB-ARC domain-containing protein miR1510a*, miR857
Onc 5026 0.0 15.7 disease resistance protein I2 miR166c
Onc 5046 26.3 70.0 uncharacterized protein LOC100279616 miR5654
Onc 5277 25.9 52.6 hypothetical protein OsI_07084 miR1510, miR5246
Onc 5425 41.1 48.2 putative disease resistance protein miR1514, miR5654
Onc 5583 119.0 203.5 hypothetical protein VITISV_018147 miR482
Onc 6091 5.2 17.7 putative disease resistance protein miR156k, miR2088, miR5654
Onc 6121 3.2 7.5 hypothetical protein OsI_15587 miR1514, miR5246
Onc 7005 58.9 62.4 putative disease resistance RPP13 protein miR1514
Onc 7221 20.1 50.3 hypothetical protein OsI_07084 miR1510a*
Onc 7977 32.2 25.1 putative disease resistance protein miR1510a*, miR5246
Onc 8764 0.0 19.9 OsJNBa0083D01.14 miR5654
Onc 8916 23.4 40.2 hypothetical protein OsI_07084 miR156k, miR5246
Onc 9873 0.0 15.9 NB-ARC domain containing protein miR1510a*, miR5246
Onc 11,319 9.1 10.6 putative disease resistance protein RGA3-like miR1514, miR5246
Onc 12,822 31.6 53.9 hypothetical protein OsI_15587 miR1510a*, miR156k
Onc 13,214 0.0 11.9 NBS-LRR protein miR1514, miR529g
Onc 15,037 0.0 9.0 NB-ARC domain containing protein miR1510a*
Onc 15,081 26.7 20.8 putative disease resistance RPP13 protein miR5246
Onc 16,931 7.8 21.2 hypothetical protein OsI_15587 miR1510a*, miR1514, miR166c, miR2088, miR5246, miR529g
Onc 19,773 6.3 0.0 putative disease resistance protein At3g14460 miR2088, miR5654
Onc 19,900 0.0 3.4 OSIGBa0148A10.13 miR5654
Onc 20,607 0.0 6.5 hypothetical protein OsJ_14506 miR838
Onc 28,117 9.1 3.6 NBS-LRR R protein miR2118
  1. Count normalized by RPKM (reads per kilobase million). CK, control RNA from uncolonized Oncidium roots; P, RNA from Pi-colonized Oncidium roots