Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps (Q28295877)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18832442%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

title

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps (English)

1 reference

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15 January 2020

1 reference

1

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15 January 2020

6

Andrew H Paterson

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15 January 2020

5

Maqsudul Alam

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15 January 2020

author name string

Xiyin Wang

series ordinal

2

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15 January 2020

John E Bowers

series ordinal

3

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15 January 2020

Ray Ming

series ordinal

4

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15 January 2020

publication date

2 October 2008

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15 January 2020

language of work or name

0 references

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15 January 2020

volume

18

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15 January 2020

issue

12

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15 January 2020

page(s)

1944-1954

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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

15 January 2020

cites work

1 reference

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Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

20 March 2017

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Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

20 March 2017

1 reference

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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

20 March 2017

1 reference

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Widespread genome duplications throughout the history of flowering plants

20 March 2017

1 reference

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Inparanoid: a comprehensive database of eukaryotic orthologs

20 March 2017

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Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

20 March 2017

1 reference

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Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes

20 March 2017

1 reference

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Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

20 March 2017

1 reference

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Darwin's abominable mystery: Insights from a supertree of the angiosperms

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

MrBayes 3: Bayesian phylogenetic inference under mixed models

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

An efficient algorithm for large-scale detection of protein families

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

MODELTEST: testing the model of DNA substitution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

PAML: a program package for phylogenetic analysis by maximum likelihood

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Basic local alignment search tool

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Aligning multiple genomic sequences with the threaded blockset aligner

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

The map-based sequence of the rice genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Extensive concerted evolution of rice paralogs and the road to regaining independence

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Gene duplication and the adaptive evolution of a classic genetic switch

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

How many genes are there in plants (... and why are they there)?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Modeling gene and genome duplications in eukaryotes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Computational approaches to unveiling ancient genome duplications

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

The lateral organ boundaries gene defines a novel, plant-specific gene family

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Phylogenetic analysis using PHYLIP.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Statistical detection of chromosomal homology using shared-gene density alone

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Synteny and Collinearity in Plant Genomes

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Positive darwinian selection at the imprinted MEDEA locus in plants

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Two ancient rounds of polyploidy in rice genome.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

DAGchainer: a tool for mining segmental genome duplications and synteny

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2593578

27 November 2018

Identifiers

DOI

10.1101/GR.080978.108

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18832442%20AND%20SRC:MED&resulttype=core&format=json

15 January 2020

1 reference

2 references

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15 January 2020

PubMed publication ID

18832442

2 references