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

Medina, Clémence; da Rocha, Martine; Magliano, Marc; Raptopoulo, Alizée; Marteu, Nathalie; Lebrigand, Kevin; Abad, Pierre; Favery, Bruno; Jaubert-Possamai, Stéphanie

doi:10.1186/s12864-018-5296-3

Table 3 siRNA DC-clusters differentially expressed in galls at 7dpi with sequence identity to Arabidopsis transposable elements

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

DC-clusters			Downstream genes			TE
Cluster name	variation G/R 7dpi	Gene name	Gene description (TAIR)	Log2 G/R 7 dpi	Similarity	TE name
chr1:10506341–10,507,511	down	At1g29980	Protein of unknown function	1.1	0.8863	BOMZH2
chr1:10506341–10,507,511	down	At1g29980	Protein of unknown function	1.1	0.9127	BOMZH2
chr1:11721631–11,721,864	up	At1g32450	Transmembrane nitrate transporter	−1.0	0.9526	ATREP4
chr1:13544313–13,545,488	down	At1g36180	acetyl-CoA carboxylase 2 acetyl-CoA carboxylase 2 (ACC2)	0.8	0.8685	ATHATN1
chr1:13544313–13,545,488	down	At1g36180	acetyl-CoA carboxylase 2 acetyl-CoA carboxylase 2 (ACC2)	0.8	0.7852	VANDAL16
chr1:9412110–9,412,695	up	At1g27100	Actin cross-linking protein	−1.2	0.8485	AtSB2
chr1:9479725–9,480,634	up	At1g27290	unknown protein	−1.1	0.8485	ATCOPIA3I
chr1:9479725–9,480,634	up	At1g27290	unknown protein	−1.1	1.0000	ATCOPIA3LTR
chr2:1281392–1,281,621	down	At2g04030	Chaperone protein htpG family	1.0	0.9291	ATREP13
chr2:14571706–14,572,100	down	At2g34590	Transketolase family protein	0.8	0.9466	ATREP1
chr2:14572190–14,572,294	down	At2g34590	Transketolase family protein	0.8	0.9505	ATREP1
chr2:15595033–15,595,856	down	At2g37120	S1FA-like DNA-binding protein	0.8	0.9756	ATMU7
chr2:15595033–15,595,856	down	At2g37120	S1FA-like DNA-binding protein	0.8	0.9863	ATMU7
chr2:8939001–8,939,617	down	At2g20750	expansin B1	0.7	0.7231	BRODYAGA1A
chr3:10284167–10,284,467	down	At3g27740	carbamoyl phosphate synthetase A	0.7	0.7131	TSCL
chr3:22214692–22,214,777	down	At3g60140	Glycosyl hydrolase superfamily protein	0.7	0.8537	AtSB2
chr4:2442915–2,443,871	down	At4g04830	methionine sulfoxide reductase B5	1.9	0.9746	VANDAL3
chr4:2444411–2,445,805	down	At4g04830	methionine sulfoxide reductase B5	1.9	0.9860	VANDAL3
chr4:5373687–5,374,187	up	At4g08455	BTB/POZ domain-containing protein	−0.9	0.6833	ATLINE1 6
chr4:6489475–6,490,728	up	At4g10500	2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein	−0.8	0.7176 0.8434	ATHAT8 ATHATN4
chr4:9035216–9,035,789	down	At4g15930	Dynein light chain type 1 family (DIN2)	1.4	0.9623	ATTIRTA1
chr5:16211264–16,212,381	down	At5g40480	embryo defective 3012	0.7	0.7356	ATREP13
chr5:16944212–16,945,214	up	At5g42380	calmodulin like 37	−1.4	0.7117	TAG1
chr5:19447678–19,447,954	down	At5g48000	cytochrome P450, family 708, subfamily A	0.8	0.9667	ATRAN
chr5:3750834–3,753,083	up	At5g11670	NADP-malic enzyme 2	−1.4	0.8554	ATHATN4

siRNA DC-clusters differentially expressed in galls compared to uninfected roots at 7 dpi located in promoter regions and with expression patterns inversely correlated with those of the associated differentially expressed genes and displaying sequence identity to A. thaliana transposable elements (TE). The upregulation (up) or down regulation (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 dpi obtained from microarrays [32, 45] were indicated

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ISSN: 1471-2164

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