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Table 1 Top ten most upregulated and downregulated siRNA DC-clusters in galls compared to uninfected roots at 7 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 7dpi gene name Gene description (TAIR) Log2 G/R
7 dpi 14 dpi 21 dpi
chr4:5373687–5,374,187 up At4g08455 BTB/POZ domain-containing protein −0.9 No − 0.9
chr1:17450567–17,451,109 up At1g47530 MATE efflux family protein −0.8 No −1.0
chr3:10387344–10,387,729 up At3g27970 Exonuclease family protein −1.1 No −0.9
chr2:11040438–11,040,725 up At2g25900 A. thaliana TANDEM ZINC FINGER PROTEIN 1 (ATCTH) −0.8 −0.8 −1.4
chr3:9814548–9,815,346 up At3g26720 glycosyl hydrolase family 38 protein −1.0 No No
chr3:22340217–22,340,552 up At3g60450 Phosphoglycerate mutase family protein −1.2 −1.4 − 1.5
chr3:15356722–15,357,007 up At3g43430 RING/U-box superfamily protein (zinc finger) −0.7 −0.9 No
chr1:25745346–25,745,737 up At1g68570 membrane localized GA transporter (ATNPF3.1) −1.2 −1.5 −1.3
chr1:24996663–24,997,231 up At1g66970 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD) LIKE 1 −0.9 −1.5 −0.9
chr2:1681688–1,682,004 up At2g04795 unknown protein −1.2 No No
chr3:10284167–10,284,467 down At3g27740 carbamoyl phosphate synthetase (CPS) small subunit (carA) 0.7 No No
chr1:26139675–26,140,148 down At1g69530 Expansin A1 1.3 2.9 3.0
chr1:10506341–10,507,511 down At1g29980 choice-of-anchor C domain protein 1.1 1.9 1.4
chr4:2442915–2,443,871 down At4g04830 methionine sulfoxide reductase B5 1.9 No No
chr3:22214692–22,214,777 down At3g60140 protein similar to beta-glucosidase 0.7 −2.1 −1.2
chr2:1281392–1,281,621 down At2g04030 chloroplast-targeted 90-kDa heat shock protein (CR88) 1.0 0.9 No
chr1:3322776–3,323,550 down At1g10140 unknown protein 0.9 No 0.7
chr5:19447678–19,447,954 down At5g48000 Member of the CYP708A family of cytochrome P450 enzymes (CYP708A2) 0.8 No No
chr2:14572190–14,572,294 down At2g34590 transketolase family protein 0.8 1.1 0.7
  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) or downregulation (down) of the cluster in galls (G) compared to uninfected roots (R) at 7 dpi (variation G/R 7 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