DOI: 10.5061/dryad.s43c7
title: Data from: Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation in Medicago truncatula

description: Nodulation (Nod) factors (NFs) are symbiotic molecules produced by
 rhizobia that are essential for establishment of the rhizobium–legume
 endosymbiosis. Purified NFs can stimulate lateral root formation (LRF) in
 Medicago truncatula, but little is known about the molecular mechanisms
 involved. Using a combination of reporter constructs, pharmacological and
 genetic approaches, we show that NFs act on early steps of LRF in M.
 truncatula, independently of the ethylene signaling pathway and of the
 cytokinin receptor MtCRE1, but in interaction with auxin. We conducted a
 whole-genome transcriptomic study upon NF and/or auxin treatments, using a
 lateral root inducible system adapted for M. truncatula. This revealed a
 large overlap between NF and auxin signaling and, more interestingly,
 synergistic interactions between these molecules. Three groups showing
 interaction effects were defined: group 1 contained more than 1500 genes
 responding specifically to the combinatorial treatment of NFs and auxin;
 group 2 comprised auxin-regulated genes whose expression was enhanced or
 antagonized by NFs; and in group 3 the expression of NF regulated genes
 was antagonized by auxin. Groups 1 and 2 were enriched in signaling and
 metabolic functions, which highlights important crosstalk between NF and
 auxin signaling for both developmental and symbiotic processes.
description: TableS1_primersTable S1: Primer pairs used for Q-PCR on the Medicago truncatula genesTable S2. List of genes differentially regulated by NAAList of genes down-regulated in the NAA condition. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. LFC: Log2 fold change. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.Table_S2_NAA.xlsxTable S3. List of genes differentially regulated by Nod FactorsTable S3. List of genes differently expressed in the NF treatment compared to control conditions. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. LFC: Log2 fold change. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.table_S3_DEG_NF.xlsxTable S4. List of genes differentially regulated by NAA+NF compared to control conditionsList of genes differently expressed in the NF+NAA treatment compared to control conditions. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. LFC: Log2 fold change. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.tableS4_NAA_and NF_DEG.xlsxTable S5. List of genes from the first synergistic groupList of genes in the first synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.TableS5_synergy_group1.xlsxTable S6. List of genes differentially regulated by NAA+NF compared to NAAList of genes differently expressed in the NF+NAA treatment compared to NAA condition. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. pval BH= p-value obtained using a Benjamini Hochberg FDR test. LFC: Log2 fold change. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.TableS6_DEGNF+NAAvsNAA.xlsxTable S7. List of genes from the second synergistic groupList of genes in the second synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.TableS7_synergy_group2vf.xlsxTable S8. List of genes with a potential hormonal or LRF functionList of differentially expressed genes with a potential hormonal function. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. All genes had a significant adjusted pvalue in at least one of the conditions tested. LFC: Log2 fold change. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.TableS8_revised.xlsxTable S9. List of genes from the third synergistic groupList of genes in the third synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.tableS9_synergy_group3.xlsx