Separating homeologs by phasing in the tetraploid wheat transcriptome

scientific article

Separating homeologs by phasing in the tetraploid wheat transcriptome is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1050836339
P356DOI10.1186/GB-2013-14-6-R66
P932PMC publication ID4053977
P698PubMed publication ID23800085
P5875ResearchGate publication ID242016086

P50authorJorge DubcovskyQ22277627
Cristobal UauyQ46744336
Eduard AkhunovQ61762947
P2093author name stringVince Buffalo
Facundo Tabbita
Stephen Pearce
Paul Bailey
Marcelo Soria
Ksenia V Krasileva
Shichen Wang
Sarah Ayling
IWGS Consortium
P2860cites workAutomated generation of heuristics for biological sequence comparisonQ21061202
Draft genome of the wheat A-genome progenitor Triticum urartuQ22122138
Analysis of the bread wheat genome using whole-genome shotgun sequencingQ22122152
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genesQ24563620
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expressionQ24608592
GENCODE: the reference human genome annotation for The ENCODE ProjectQ24608743
Full-length transcriptome assembly from RNA-Seq data without a reference genomeQ24620766
The Pfam protein families databaseQ24644670
BLAT—The BLAST-Like Alignment ToolQ24682492
Basic local alignment search toolQ25938991
CAP3: A DNA sequence assembly programQ27860964
The transcriptional landscape of the mammalian genomeQ27861110
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication eventsQ28186749
HapCUT: an efficient and accurate algorithm for the haplotype assembly problemQ45832910
Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spacesQ46962713
Molecular evidence for Triticum speltoides as a B-genome progenitor of wheat (Triticum aestivum).Q51116718
Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheatQ59203365
The evolution of polyploid wheats: identification of the A genome donor speciesQ81249311
Genome evolution due to allopolyploidization in wheatQ28710327
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequencesQ29547172
Accelerated Profile HMM SearchesQ29547576
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomicsQ29616221
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTsQ29617281
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levelsQ29617522
Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheatQ30000859
BAC libraries of Triticum urartu, Aegilops speltoides and Ae. tauschii, the diploid ancestors of polyploid wheatQ33223757
Wheat FT protein regulates VRN1 transcription through interactions with FDL2.Q33345497
A physical map of the 1-gigabase bread wheat chromosome 3B.Q33373632
The role of hybridization in plant speciationQ33477947
A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheatQ33497643
Small RNAs, DNA methylation and transposable elements in wheatQ33618598
De novo assembly and analysis of RNA-seq data.Q33714197
Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levelsQ33736252
Haplotype-resolved genome sequencing of a Gujarati Indian individual.Q33775428
Strobe sequence design for haplotype assemblyQ33826943
Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencingQ33865193
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenesQ33891354
Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomesQ33924167
Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheatQ34031511
Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescenceQ34043872
Population genomics and local adaptation in wild isolates of a model microbial eukaryoteQ34161788
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plantsQ34195296
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organismsQ34342682
Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq dataQ34379264
Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat.Q34417744
Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance geneQ34546680
Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chlorideQ34586452
Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination ratesQ35978427
Contrasting rates of evolution in Pm3 loci from three wheat species and riceQ36083274
Genome plasticity a key factor in the success of polyploid wheat under domesticationQ36864536
Evolutionary genetics of genome merger and doubling in plantsQ37317018
TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomicsQ38510142
Deletion polymorphism in wheat chromosome regions with contrasting recombination ratesQ42014998
Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relativesQ43461505
Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B.Q43502291
P4510describes a project that usesMIRAQ114076742
P433issue6
P921main subjecttranscriptomeQ252857
wheatQ15645384
P304page(s)R66
P577publication date2013-06-25
P1433published inGenome BiologyQ5533480
P1476titleSeparating homeologs by phasing in the tetraploid wheat transcriptome
P478volume14

Reverse relations

cites work (P2860)
Q37298744A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea.
Q58603591A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Q29029314A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
Q35145839A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.).
Q36908336A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains
Q40405309An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha).
Q37357785Analysing complex Triticeae genomes - concepts and strategies.
Q55417488Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium.
Q64968956Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding.
Q37595949Biofortification of wheat grain with iron and zinc: integrating novel genomic resources and knowledge from model crops
Q33358217Characterization of FLOWERING LOCUS T1 (FT1) gene in Brachypodium and wheat
Q35116517Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana
Q55483602Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes.
Q47635959Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660K SNP array reveals a homoeologous relationship with the wheat genome
Q35913385De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection
Q35640613De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens
Q37080993De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.).
Q58612022De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation
Q33742441De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock
Q38464178De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat
Q42845081Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat
Q89818826Dissecting the Genetic Complexity of Fusarium Crown Rot Resistance in Wheat
Q93067416Effects of different nitrogen fertilizers on two wheat cultivars: An integrated approach
Q50074992Enabling Molecular Technologies for Trait Improvement in Wheat.
Q33364542Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study.
Q31036771FRAMA: from RNA-seq data to annotated mRNA assemblies
Q33361282Factorial combinations of protein interactions generate a multiplicity of florigen activation complexes in wheat and barley
Q37564135Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat
Q36157030Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Q37100187Genetic and physical mapping of the earliness per se locus Eps-A (m) 1 in Triticum monococcum identifies EARLY FLOWERING 3 (ELF3) as a candidate gene.
Q64057973Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Q30976585Genomics as the key to unlocking the polyploid potential of wheat
Q41684572Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm
Q35682554Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family
Q26750493Homoeologs: What Are They and How Do We Infer Them?
Q47208939Increased pericarp cell length underlies a major quantitative trait locus for grain weight in hexaploid wheat
Q36653775Large deletions in the CBF gene cluster at the Fr-B2 locus are associated with reduced frost tolerance in wheat
Q46292684Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop
Q35763390Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing
Q35574938Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms
Q35531989Pattern and process in the evolution of the sole dioecious member of Brassicaceae.
Q46834533Population transcriptomics reveals a potentially positive role of expression diversity in adaptation
Q36911072RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.).
Q33358634RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
Q34998731Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence
Q35861321Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes
Q91341451Resistance gene cloning from a wild crop relative by sequence capture and association genetics
Q38391092SNP genotyping and population genomics from expressed sequences - current advances and future possibilities
Q42639863Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas
Q35640030Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes
Q38759244Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing.
Q36605460Transcriptome Analysis Identifies Candidate Genes Related to Triacylglycerol and Pigment Biosynthesis and Photoperiodic Flowering in the Ornamental and Oil-Producing Plant, Camellia reticulata (Theaceae)
Q37373021Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating Salix integra
Q28817754Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability
Q35805180Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars
Q37716812Transcriptomic Profiles Reveal the Interactions of Cd/Zn in Dwarf Polish Wheat (Triticum polonicum L.) Roots
Q36175545Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe
Q37640382Uncovering hidden variation in polyploid wheat
Q37377601Unlocking Triticeae genomics to sustainably feed the future
Q51549681Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes.
Q34089300Wheat TaNPSN SNARE homologues are involved in vesicle-mediated resistance to stripe rust (Puccinia striiformis f. sp. tritici).
Q46241265Wheat genetic resources in the post-genomics era: promise and challenges
Q30488940expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.

Search more.