LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

[A. thaliana (gene)]
Detail of Experiment mapped on Arabidopsis thaliana col Araport11

Details

Name	Arabidopsis RNA-Seq data upon inoculation with commensal Rhizobiales R129E
Description	Rhizobia are a paraphyletic group of soil-borne bacteria characterized by their ability to induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species within the Rhizobiales order define a core lineage of the plant microbiota, suggesting alternative forms of interactions with plant hosts. Genome analysis of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota showed that key symbiosis genes were acquired multiple times and that their most recent common ancestor had the capacity to colonize the roots of a broad range of hosts. We identify root growth promotion as a characteristic trait of Rhizobiales in Arabidopsis thaliana, whereas interference with the plant immune system constitutes a separate, strain-specific phenotype of root commensal Alphaproteobacteria. Using a tripartite gnotobiotic plant system, we show that these traits operate in a modular fashion and might be relevant to microbial homeostasis in healthy roots.
Contact	MPIPZ
Xref	PRJEB27007
Reference	Garrido-Oter R et al . 2018;
Conditions	16
Species	Arabidopsis thaliana
Metadata export	.CSV .JSON

Analysis

Mapped Genomes	Araport11
Expression Analysis	Expression Profile / Differential Expression / Co-expression

Conditions

Name	Genotype	Mutation	Stage	Tissue	Treatment	Level	Time	Samples	Xref	Download alignments
noP_350_d12	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 12 dpi under phosphate-deficient condition.			noP_350_d12_1 noP_350_d12_2 noP_350_d12_3	ERR2617009 ERR2617010 ERR2617011	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_350_d16	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 16 dpi under phosphate-deficient condition.			noP_350_d16_1 noP_350_d16_2 noP_350_d16_3	ERR2617021 ERR2617022 ERR2617023	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_350_d4	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 4 dpi under phosphate-deficient condition.			noP_350_d4_1 noP_350_d4_2 noP_350_d4_3	ERR2617032 ERR2617033 ERR2617034	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_350_d8	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 8 dpi under phosphate-deficient condition.			noP_350_d8_1 noP_350_d8_2 noP_350_d8_3	ERR2617044 ERR2617045 ERR2617046	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_MgCl_d12	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 12 dpi under phosphate-deficient condition.			noP_MgCl_d12_1 noP_MgCl_d12_2 noP_MgCl_d12_3	ERR2617003 ERR2617004 ERR2617005	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_MgCl_d16	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 16 dpi under phosphate-deficient condition.			noP_MgCl_d16_1 noP_MgCl_d16_2 noP_MgCl_d16_3	ERR2617015 ERR2617016 ERR2617017	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_MgCl_d4	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 4 dpi under phosphate-deficient condition.			noP_MgCl_d4_1 noP_MgCl_d4_2 noP_MgCl_d4_3	ERR2617026 ERR2617027 ERR2617028	.bam .bai .csi .bam .bai .csi .bam .bai .csi
noP_MgCl_d8	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 8 dpi under phosphate-deficient condition.			noP_MgCl_d8_1 noP_MgCl_d8_2 noP_MgCl_d8_3	ERR2617038 ERR2617039 ERR2617040	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_350_d12	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 12 dpi under phosphate-rich condition.			P_350_d12_1 P_350_d12_2 P_350_d12_3	ERR2617006 ERR2617007 ERR2617008	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_350_d16	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 16 dpi under phosphate-rich condition.			P_350_d16_1 P_350_d16_2 P_350_d16_3	ERR2617018 ERR2617019 ERR2617020	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_350_d4	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 4 dpi under phosphate-rich condition.			P_350_d4_1 P_350_d4_2 P_350_d4_3	ERR2617029 ERR2617030 ERR2617031	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_350_d8	Col-0		vegetative	root	Rhizobium 129E treated Col-0 roots. 8 dpi under phosphate-rich condition.			P_350_d8_1 P_350_d8_2 P_350_d8_3	ERR2617041 ERR2617042 ERR2617043	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_MgCl_d12	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 12 dpi under phosphate-rich condition.			P_MgCl_d12_1 P_MgCl_d12_2 P_MgCl_d12_3	ERR2617047 ERR2617048 ERR2617002	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_MgCl_d16	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 16 dpi under phosphate-rich condition.			P_MgCl_d16_1 P_MgCl_d16_2 P_MgCl_d16_3	ERR2617012 ERR2617013 ERR2617014	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_MgCl_d4	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 4 dpi under phosphate-rich condition.			P_MgCl_d4_1 P_MgCl_d4_2 P_MgCl_d4_3	ERR2617001 ERR2617024 ERR2617025	.bam .bai .csi .bam .bai .csi .bam .bai .csi
P_MgCl_d8	Col-0		vegetative	root	mock (10 mM MgCl2) treated Col-0 roots. 8 dpi under phosphate-rich condition.			P_MgCl_d8_1 P_MgCl_d8_2 P_MgCl_d8_3	ERR2617035 ERR2617036 ERR2617037	.bam .bai .csi .bam .bai .csi .bam .bai .csi