19 Result(s)
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Article
Open AccessGET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define...
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Protocol
Pangenome Analysis of Plant Transcripts and Coding Sequences
The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for...
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Protocol
Scripting Analyses of Genomes in Ensembl Plants
Ensembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species ...
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Article
Open AccessFine-tuning of the flowering time control in winter barley: the importance of HvOS2 and HvVRN2 in non-inductive conditions
In winter barley plants, vernalization and photoperiod cues have to be integrated to promote flowering. Plant development and expression of different flowering promoter (HvVRN1, HvCO2, PPD-H1, HvFT1, HvFT3) and r...
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Article
Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike
Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and ha...
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Protocol
FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces
FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematic...
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Protocol
RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes
In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protoco...
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Protocol
RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes
The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu) offers specialized options for researchers dealing with plant tr...
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Article
BARLEYMAP: physical and genetic map** of nucleotide sequences and annotation of surrounding loci in barley
The BARLEYMAP pipeline was designed to map both genomic sequences and transcripts against sequence-enriched genetic/physical frameworks, with plant breeders as the main target users. It reports the most proba...
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Article
Selection footprints in barley breeding lines detected by combining genoty**-by-sequencing with reference genome information
This study is a retrospective analysis of an elite cross from the Spanish National Barley Breeding Program. This was the most successful cross produced in the breeding program in the past 20 years. The progeny...
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Protocol
Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids
GET_HOMOLOGUES is an open-source software package written in Perl and R to define robust core- and pan-genomes by computing consensus clusters of orthologous gene families from whole-genome sequences using the...
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Article
Open AccessIntegrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes
Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting w...
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Article
Fine map** of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces
In two Spanish barley landraces with outstanding resistance to scald, the Rrs1 Rh4 locus was fine ...
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Article
Open AccessGenetic recombination is associated with intrinsic disorder in plant proteomes
Intrinsically disordered proteins, found in all living organisms, are essential for basic cellular functions and complement the function of ordered proteins. It has been shown that protein disorder is linked t...
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Article
OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors
High salinity causes remarkable losses in rice productivity worldwide mainly because it inhibits growth and reduces grain yield. To cope with environmental changes, plants evolved several adaptive mechanisms, ...
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Article
Open AccessProtein disorder in plants: a view from the chloroplast
The intrinsically unstructured state of some proteins, observed in all living organisms, is essential for basic cellular functions. In this field the available information from plants is limited but it has bee...
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Article
HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys
In barley, three genes are responsible for the vernalization requirement: VrnH1, VrnH2 and VrnH3. The winter growth habit of barley requires the presence of a recessive VrnH1 allele, together with an active VrnH2
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Article
Open AccessEvolutionary divergence of chloroplast FAD synthetase proteins
Flavin adenine dinucleotide synthetases (FADSs) - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN) and its subsequent adeny...
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Article
Open AccessPrediction of TF target sites based on atomistic models of protein-DNA complexes
The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding spe...
