(Q46962713)

26 December 2017

title

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

1 reference

26 December 2017

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12

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26 December 2017

Frédéric Choulet

Frédéric Choulet

1

0 references

Michael Pumphrey

Michael Pumphrey

14

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Arnaud Couloux

Arnaud Couloux

11

0 references

Bikram S Gill

21

Bikram S Gill

1 reference

26 December 2017

2

Thomas Wicker

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26 December 2017

James Breen

13

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Catherine Feuillet

24

Catherine Feuillet

1 reference

26 December 2017

23

Beat Keller

1 reference

26 December 2017

Rudi Appels

22

Rudi Appels

1 reference

26 December 2017

Philippe Leroy

6

Philippe Leroy

1 reference

26 December 2017

Jizeng Jia

17

Jizeng Jia

1 reference

26 December 2017

Xiuying Kong

16

Xiuying Kong

1 reference

26 December 2017

Camille Rustenholz

3

Camille Rustenholz

1 reference

26 December 2017

Marie-Christine Le Paslier

8

Marie-Christine Le Paslier

1 reference

26 December 2017

author name string

Etienne Paux

4

1 reference

26 December 2017

Jérome Salse

5

1 reference

26 December 2017

Stéphane Schlub

7

1 reference

26 December 2017

Ghislaine Magdelenat

9

1 reference

26 December 2017

Catherine Gonthier

10

1 reference

26 December 2017

Sixin Liu

15

1 reference

26 December 2017

Marta Gut

18

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26 December 2017

Dominique Brunel

19

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26 December 2017

James A Anderson

20

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26 December 2017

publication date

25 June 2010

1 reference

26 December 2017

published in

The Plant Cell

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26 December 2017

volume

22

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26 December 2017

issue

6

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26 December 2017

page(s)

1686-1701

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26 December 2017

Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat

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1 reference

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29 September 2018

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29 September 2018

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Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs

29 September 2018

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Polyploidy and genome restructuring: a variety of outcomes

29 September 2018

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Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

29 September 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

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Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

29 September 2018

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Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize

29 September 2018

1 reference

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TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The Sorghum bicolor genome and the diversification of grasses

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A physical map of the 1-gigabase bread wheat chromosome 3B.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Acc homoeoloci and the evolution of wheat genomes

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Transcriptional and metabolic adjustments in ADP-glucose pyrophosphorylase-deficient bt2 maize kernels

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A unified classification system for eukaryotic transposable elements

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Clustal W and Clustal X version 2.0

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A GeneTrek analysis of the maize genome

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Gene evolution at the ends of wheat chromosomes

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Structure and architecture of the maize genome.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Differential methylation of genes and repeats in land plants

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The map-based sequence of the rice genome

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Identification of genes preferentially expressed during wood formation in Eucalyptus

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Sequence composition, organization, and evolution of the core Triticeae genome

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Pack-MULE transposable elements mediate gene evolution in plants

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Sequence composition and genome organization of maize.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Rapid recent growth and divergence of rice nuclear genomes

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Demarcating the gene-rich regions of the wheat genome

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

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

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Comparative DNA sequence analysis of wheat and rice genomes

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the triticeae

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Artemis: sequence visualization and annotation

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The paleontology of intergene retrotransposons of maize

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Consed: a graphical tool for sequence finishing

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Base-calling of automated sequencer traces using phred. II. Error probabilities

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The distribution of genes in the genomes of Gramineae.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

The gene distribution of the maize genome.

29 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2910976

Homoeologous gene silencing in hexaploid wheat

29 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20581307

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20581307

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20581307

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1105/TPC.110.074187

1 reference

26 December 2017

0 references

1 reference

26 December 2017