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

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Name Description Contact Reference Conditions
Gene expression profiling of the octuple jazQ mycT mutant The quintuple jaz mutant jazQ and the triple myc mutant mycT affect plant defense and growth. We used RNA-sequencing to query the transcriptomes of jazQ and mycT, as well as the combined jazQ mycT octuple mutatant, and examined how these mutations alter the expression of genes mis-regulated in jazQ. The data highlight how jasmonate signaling pathways are largely governed by MYC transcription factors, but also highlight some MYC-independent expression patterns. Overall design: Analysis of Col-0 (......[More] Plant Research Laboratory, Michigan State University 4
Transcriptome profiling of ozone responses of Arabidopsis thaliana Many Arabidopsis thaliana accession show sensitvity to the air pollutant ozone, including the accession Cvi-0 from the Cape Verde Islands. To understand and assist in genetic mapping of loci causing the ozone sensitvity of Cvi-0, transcript profiling was performed in Cvi-0, the tolerant Col-0, and a near isogenic line (Col-S) where ozone sensitivity was introgressesed from Cvi-0 to Col-0 through eight rounds of backcrossing. Overall design: The near isogenic line Col-S and its parents Col-0 and ......[More] University of Helsinki
Combining chemical and genetic approaches to increase drought resistance in plants Using RNA-Seq to analyse the gene expression pattern induced by ABA and two artificial analogs in wild type (Col-0) Arabidopsis plants Overall design: RNA-Seq: 3-week-old Col-0 plants, sprayed with DMSO (control) or 10μM ABA/AMF1beta/AMF4 and sampled 6,24 or 72hours after treatment. Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences 12
DNA replication-coupled histone modification maintains Polycomb gene silencing in plants Propagation of patterns of gene expression through the cell cycle requires prompt restoration of epigenetic marks after the twofold dilution caused by DNA replication. Here, we show that the transcriptional repressive mark histone H3K27 trimethylation (H3K27me3) is restored in replicating plant cells through DNA replication-coupled modification of histone variant H3.1. Plants evolved a mechanism for efficient K27 trimethylation on H3.1, which is essential for inheritance of the silencing memory ......[More] Gregor Mendel Institute 3
Genomic architecture of biomass heterosis in Arabidopsis Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an ......[More] Peiking University 2
Genome-wide analysis of specific alterations in transcript structure and accumulation caused by nutrient deficiencies in Arabidopsis thaliana. Alteration of transcript structure represents an important step of regulation of gene function. To analyze genome wide response of exon combination patterns under nutrient deficiencies in plants, we performed paired-end RNA sequencing (illumine HiSeq2000) for the roots of Arabidopsis thaliana (Col-0) exposed to deficiencies of 12 different nutrients (N, K, Ca, Mg, P, S, B, Fe, Mn, Zn, Cu, Mo) and un-exposed control plants. Transcripts were assembled and quantified, and the relative abundances of......[More] Graduate School of Agricultural and Life Sciences , the University of Tokyo 13
RNASequencing of nf-yc, nf-yb, and CO-SAIL mutants during photomorphogenic growth in Arabidopsis thaliana. The purpose of this RNA Sequencing project was to investigate the transcriptional regulatory relationship between NF-YC3/4/9, NF-YB2/B3 and CO-SAIL. Methods: Total RNA was isolated, and then poly-A purified. 100ng of starting RNA was used to generate RNASeq libraries using the NEXTflex Illumina qRNA-Seq Library Prep Kit, and sequenced on an Illumina HiSeq2500 machine. Results: NF-YC3/4/9, NF-YB2/B3 and CO-SAIL have both shared and independent regulatory targets. Overall design: mRNA profiles of ......[More] BioCI
RNAseq data for Arabidopsis TF mutants during germination RNAseq profiling of eight transcription factor mutants during germination in Arabidopsis, at 24 h in the light (after 48h of stratification). Overall design: Total RNA was extracted from 50-100 mg Arabidopsis seeds in duplicates. Baulcombe lab, Department of Plant Sciences, University of Cambridge 9
Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature. ngs2015_05_high_temperature_root-high temp wt - characterize changes in root gene expression associated with plant growth at higher temperature - plants were grown at 21°C or 26°C, 16h light (90µE)/8h dark for 10 days before harveting roots. Overall design: 6 samples with 3 biological replicats. treated vs untreated comparison IPS2, INRA - CNRS – UPSUD 2
LUC7 is an U1snRNP component that plays a role in alternative splicing and terminal introns removal in plants Introns are removed by the spliceosome, a large complex composed of five ribonucleoprotein subcomplexes (U snRNP). In metazoans, the U1 snRNP, which binds to 5’ splice sites, also fulfills regulatory roles in splice site selection and possesses non-splicing related functions. Here, we show that an Arabidopsis U1 snRNP subunit, LUC7, affects constitutive and alternative splicing. Interestingly, LUC7 specifically promotes splicing of a subset of terminal introns. Splicing of LUC7-dependent termina......[More] MPIPZ 2
Coevolution of hormone metabolism and signaling networks expands plant adaptive plasticity Differential transcriptomic analysis of 10-day-old Arabidopsis seedlings treated with 50 μM ABA, PA, or DPA. Overall design: 10-day-old Arabidopsis seedlings grown on MS medium was treated with 50 μM ABA, PA, or DPA. Total RNA was extracted from biological duplicates, Illumina RNAseq was performed on each sample. Whitehead Institute for Biomedical Research 4
Arabidopsis RNA-Seq data upon inoculation with commensal Rhizobiales R129E 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 mu......[More] MPIPZ 16
Arabidopsis tissue atlas We used state of the art mass spectrometry and RNA sequencing (RNA-Seq) to provide the first integrated proteomic, phosphoproteomic and transcriptomic atlas of Arabidopsis. For this we measured 30 different Arabidopsis tissues from adult plants, seedlings, callus and cell culture samples to an average depth of 17,603 +/- 1,317 transcripts, 14,430 +/- 911 proteins and 14,689 +/- 2,509 phosphorylation sites. In total we provide protein expression data for 66 % and transcript expression data for 90......[More] Technical University Munich 55