Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. (Q33394747)

26 July 2017

Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. (English)

1 reference

26 July 2017

19

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26 July 2017

16

Jeffrey L Bennetzen

1 reference

26 July 2017

14

Andrea Zuccolo

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26 July 2017

12

Chuanzhu Fan

1 reference

26 July 2017

10

Kristi Collura

1 reference

26 July 2017

3

Abhijit Sanyal

1 reference

26 July 2017

7

Ana Clara Pontaroli

1 reference

26 July 2017

8

Teri Rambo

1 reference

26 July 2017

11

Jayson Talag

1 reference

26 July 2017

Jetty S S Ammiraju

1

1 reference

26 July 2017

Fei Lu

2

1 reference

26 July 2017

Yeisoo Yu

4

1 reference

26 July 2017

Xiang Song

5

1 reference

26 July 2017

Ning Jiang

6

1 reference

26 July 2017

Jennifer Currie

9

1 reference

26 July 2017

Jose Luis Goicoechea

13

1 reference

26 July 2017

Jinfeng Chen

15

1 reference

26 July 2017

Mingsheng Chen

17

1 reference

26 July 2017

Scott Jackson

18

1 reference

26 July 2017

19 December 2008

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26 July 2017

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26 July 2017

20

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26 July 2017

12

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26 July 2017

3191-3209

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Creative Commons Attribution-NonCommercial 4.0 International

26 July 2017

start time

19 January 2021

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Synteny and Collinearity in Plant Genomes

1 reference

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A phylogenetic analysis of indel dynamics in the cotton genus

31 October 2018

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Analysis of 142 genes resolves the rapid diversification of the rice genus

31 October 2018

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Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

31 October 2018

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Characterization of paralogous protein families in rice

31 October 2018

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Towards a better bowl of rice: assigning function to tens of thousands of rice genes

31 October 2018

1 reference

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The Rice Annotation Project Database (RAP-DB): 2008 update

31 October 2018

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Evolution of genes and genomes on the Drosophila phylogeny

31 October 2018

1 reference

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Genetic variation of NBS-LRR class resistance genes in rice lines

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Transposable element distribution, abundance and role in genome size variation in the genus Oryza

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Genome plasticity a key factor in the success of polyploid wheat under domestication

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium).

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress

31 October 2018

1 reference

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Patterns in grass genome evolution

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The molecular genetics of crop domestication

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Leafing through the genomes of our major crop plants: strategies for capturing unique information

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Concerted and birth-and-death evolution of multigene families

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Chromosome evolution in eukaryotes: a multi-kingdom perspective

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The map-based sequence of the rice genome

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The Genomes of Oryza sativa: a history of duplications

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Mechanisms of recent genome size variation in flowering plants

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Pack-MULE transposable elements mediate gene evolution in plants

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Rapid recent growth and divergence of rice nuclear genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

VISTA: computational tools for comparative genomics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Comparisons of pollen coat genes across Brassicaceae species reveal rapid evolution by repeat expansion and diversification

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Comparative genetics at the gene and chromosome levels between rice ( Oryza sativa) and wildrice ( Zizania palustris).

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Diversity in the Oryza genus

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Apollo: a sequence annotation editor

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

An active DNA transposon family in rice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Contiguous genomic DNA sequence comprising the 19-kD zein gene family from maize

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

BLAT—The BLAST-Like Alignment Tool

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Phylogeny of rice genomes with emphasis on origins of allotetraploid species

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae).

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Colinearity and its exceptions in orthologous adh regions of maize and sorghum

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

MODELTEST: testing the model of DNA substitution

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The paleontology of intergene retrotransposons of maize

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Consed: a graphical tool for sequence finishing

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Rapid reorganization of resistance gene homologues in cereal genomes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Alien introgression in rice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Evolution by the birth-and-death process in multigene families of the vertebrate immune system

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Gene identification in a complex chromosomal continuum by local genomic cross-referencing.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Molecular evolution of the Adh1 locus in the genus Zea.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Molecular evolution of alcohol dehydrogenase 1 in members of the grass family

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

The rapid generation of mutation data matrices from protein sequences

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630430

Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19098269

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genome-wide investigation on the genetic variations of rice disease resistance genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19098269

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Confidence Limits on Phylogenies: an Approach using the Bootstrap

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19098269

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1105/TPC.108.063727

1 reference

26 July 2017

0 references

1 reference