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Table 2 Top ten most upregulated siRNA DC-clusters in galls compared to uninfected roots at 14 dpi

From: Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

DC-clusters Downstream genes
Cluster name variation G/R 14 dpi gene name Gene description (TAIR) Log2 G/R
7 dpi 14 dpi 21 dpi
chr1:25745518–25,745,718 up At1g68570 Membrane localized GA transporter (NPF3.1) −1.2 − 1.5 −1.3
chr1:9412541–9,412,703 up At1g27100 Actin crosslinking protein −1.2 −0.9 −1.0
chr2:18703172–18,703,490 up At2g45380 Myeloid leukemia factor No −1.1 −1.6
chr4:1063076–1,063,502 up At4g02410 Concanavalin A-like lectin protein kinase family No −0.7 − 0.6
chr5:16944206–16,944,689 up At5g42380 Calmodulin like 37 (CML37) −1.4 −2.0 −2.4
chr3:17722355–17,722,693 up At3g48020 Hypothetical protein No −0.8 −0.8
chr5:14896137–14,896,289 up At5g37500 Gated outwardly-rectifying K+ channel No −0.7 − 0.6
chr4:8677540–8,679,013 up At4g15230 Pleiotropic drug resistance 2 (PDR2); ATPase No −1.0 −0.7
chr1:23262107–23,262,634 up At1g62810 Copper amineoxidase 1 (CuAO1) No −1.3 No
chr4:7855461–7,857,189 up At4g13510 Plasma membrane localized ammonium transporter (AMT1;1) −0.7 −1.0 −0.6
  1. These DC-clusters were all shared by galls and roots and located in promoter regions and with expression patterns inversely correlated with those of the downstream differentially expressed genes. The upregulation (up) of the cluster in galls (G) compared to uninfected roots (R) at 14 dpi (variation G/R 14 dpi), the AGI gene name, the description of the encoded protein from TAIR and the log2 values of galls/roots at 7, 14 and 21 dpi obtained from microarrays [32, 45] were indicated