Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat (Q59203365)

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English	Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat	article

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Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat (English)

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Jaroslav Doležel

object named as

Jaroslav Dolezel

15

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10

object named as

Hana Simková

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16

object named as

Bikram S Gill

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Gaganpreet Kaur

6

object named as

Gaganpreet Kaur

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13

object named as

Mingcheng Luo

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Sunish K. Sehgal

2

object named as

Sunish Sehgal

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1

object named as

Eduard D Akhunov

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Kerrie L. Forrest

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object named as

Kerrie L Forrest

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author name string

Hanquan Liang

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Shichen Wang

4

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Alina R Akhunova

5

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Wanlong Li

7

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Deven See

9

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Yaqin Ma

11

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Matthew J Hayden

12

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Justin D Faris

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publication date

January 2013

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Plant Physiology

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161

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1

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252-65

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copyright license

Creative Commons Attribution 4.0 International

27 January 2021

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April 2022 Public Data File from Crossref

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The advantages and disadvantages of being polyploid

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Preservation of duplicate genes by complementary, degenerative mutations

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The gene balance hypothesis: from classical genetics to modern genomics

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat

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Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Adaptive evolution of young gene duplicates in mammals.

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Chromosome-based genomics in the cereals

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https://pubmed.ncbi.nlm.nih.gov/23124323

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A starch-branching enzyme gene in wheat produces alternatively spliced transcripts

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https://pubmed.ncbi.nlm.nih.gov/23124323

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BLAT—The BLAST-Like Alignment Tool

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https://pubmed.ncbi.nlm.nih.gov/23124323

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High rate of chimeric gene origination by retroposition in plant genomes.

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris

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The maize genome contains a helitron insertion

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Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome.

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A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

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Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces

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https://pubmed.ncbi.nlm.nih.gov/23124323

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A codon-based model of nucleotide substitution for protein-coding DNA sequences

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Patching gaps in plant genomes results in gene movement and erosion of colinearity

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Grass genome organization and evolution

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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https://pubmed.ncbi.nlm.nih.gov/23124323

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RNA-based gene duplication: mechanistic and evolutionary insights

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Structure and evolution of cereal genomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Allopolyploidization reduces alternative splicing efficiency for transcripts of the wheat DREB2 homolog, WDREB2.

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat.

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Acc homoeoloci and the evolution of wheat genomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Unlocking the barley genome by chromosomal and comparative genomics

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Constraints and plasticity in genome and molecular-phenome evolution

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The B73 Maize Genome: Complexity, Diversity, and Dynamics

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Extensive structural renovation of retrogenes in the evolution of the Populus genome

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Origin and early evolution of angiosperms

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics

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https://pubmed.ncbi.nlm.nih.gov/23124323

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PAML 4: phylogenetic analysis by maximum likelihood

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Alternative splicing of pre-messenger RNAs in plants in the genomic era.

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Correlation between sequence conservation and the genomic context after gene duplication.

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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The Sorghum bicolor genome and the diversification of grasses

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The "alternative" choice of constitutive exons throughout evolution

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The map-based sequence of the rice genome

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Genome-wide analyses of alternative splicing in plants: opportunities and challenges.

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Homoeolog-specific transcriptional bias in allopolyploid wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The origin of new genes: glimpses from the young and old

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The evolution of polyploid wheats: identification of the A genome donor species

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Flow karyotyping and chromosome sorting in bread wheat ( Triticum aestivum L.).

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https://pubmed.ncbi.nlm.nih.gov/23124323

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HyPhy: hypothesis testing using phylogenies

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Variation for homoeologous gene silencing in hexaploid wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae.

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Genome sequencing and analysis of the model grass Brachypodium distachyon

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https://pubmed.ncbi.nlm.nih.gov/23124323

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How did alternative splicing evolve?

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Gene loss, silencing and activation in a newly synthesized wheat allotetraploid.

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Understanding mechanisms of novel gene expression in polyploids

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The evolutionary fate and consequences of duplicate genes

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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The evolutionary significance of ancient genome duplications

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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Genomewide comparative analysis of alternative splicing in plants

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs

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https://pubmed.ncbi.nlm.nih.gov/23124323

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The evolution of functionally novel proteins after gene duplication.

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https://pubmed.ncbi.nlm.nih.gov/23124323

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RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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The origin of Triticum spelta and its free-threshing hexaploid relatives

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

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https://pubmed.ncbi.nlm.nih.gov/23124323

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Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice

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https://pubmed.ncbi.nlm.nih.gov/23124323

12 December 2020

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10.1104/PP.112.205161

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