Expansion by whole genome duplication and evolution of the sox gene family in teleost fish (Q38664830)

5 September 2017

Expansion by whole genome duplication and evolution of the sox gene family in teleost fish (English)

1 reference

5 September 2017

whole genome duplication

1 reference

based on heuristic

inferred from title

whole genome sequencing

1 reference

4

Jean-Nicolas Volff

0 references

Frédéric Brunet

2

object named as

Frédéric Brunet

0 references

author name string

Emilien Voldoire

1

1 reference

5 September 2017

Magali Naville

3

1 reference

5 September 2017

Jean-Nicolas Volff

4

1 reference

5 September 2017

Delphine Galiana

5

1 reference

5 September 2017

language of work or name

English

0 references

publication date

24 July 2017

1 reference

5 September 2017

1 reference

5 September 2017

12

1 reference

5 September 2017

e0180936

1 reference

5 September 2017

7

1 reference

Creative Commons Attribution 4.0 International

5 September 2017

start time

24 July 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The genomic substrate for adaptive radiation in African cichlid fish

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The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

6 September 2017

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Flower diversity and angiosperm diversification

6 September 2017

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The sox family of transcription factors: versatile regulators of stem and progenitor cell fate

6 September 2017

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Whole-genome duplication and the functional diversification of teleost fish hemoglobins

6 September 2017

1 reference

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Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication

6 September 2017

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Angiosperm diversification through time

6 September 2017

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Polyploidy and angiosperm diversification

6 September 2017

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Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes

6 September 2017

1 reference

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Origins, evolution, and phenotypic impact of new genes.

6 September 2017

1 reference

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Pigmentation pathway evolution after whole-genome duplication in fish

6 September 2017

1 reference

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The evolution of gene duplications: classifying and distinguishing between models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Chordate roots of the vertebrate nervous system: expanding the molecular toolkit

6 September 2017

1 reference

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The evolutionary significance of ancient genome duplications

6 September 2017

1 reference

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No backbone but lots of Sox: Invertebrate Sox genes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.

6 September 2017

1 reference

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Turning a hobby into a job: how duplicated genes find new functions

6 September 2017

1 reference

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Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Organization of conserved elements near key developmental regulators in vertebrate genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Consequences of genome duplication

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

The evolutionary consequences of polyploidy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Clustal W and Clustal X version 2.0

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

The medaka draft genome and insights into vertebrate genome evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

PAML 4: phylogenetic analysis by maximum likelihood

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Ancient noncoding elements conserved in the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Genome duplication and the origin of angiosperms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis

6 September 2017

1 reference

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Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Sex chromosome specialization and degeneration in mammals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Many genes in fish have species-specific asymmetric rates of molecular evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Two rounds of whole genome duplication in the ancestral vertebrate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Subfunctionalization of duplicated genes as a transition state to neofunctionalization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Genome evolution and biodiversity in teleost fish

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Subfunction partitioning, the teleost radiation and the annotation of the human genome.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Stages of normal development in the medaka Oryzias latipes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Origin and diversity of the SOX transcription factor gene family: genome-wide analysis in Fugu rubripes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Genome duplication, subfunction partitioning, and lineage divergence:Sox9in stickleback and zebrafish

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Dosage sensitivity and the evolution of gene families in yeast

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

The 2R hypothesis and the human genome sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Yesterday's polyploids and the mystery of diploidization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

The evolutionary fate and consequences of duplicate genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Zebrafish hox clusters and vertebrate genome evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Stages of embryonic development of the zebrafish

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Mutational analysis of SRY in XY females

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Basic local alignment search tool

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

A second form of Sox11 homologue identified in the orange-spotted grouper Epinephelus coioides: analysis of sequence and mRNA expression patterns

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

The zebrafish gene map defines ancestral vertebrate chromosomes

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Expression of sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Transcriptional divergence of the duplicated hypoxia-inducible factor alpha genes in zebrafish.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

A homologue of Sox11 predominantly expressed in the ovary of the orange-spotted grouper Epinephelus coioides

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

A Mathematical Theory of Natural and Artificial Selection Part X. Some Theorems on Artificial Selection

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Rearrangement rate following the whole-genome duplication in teleosts.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

sox4b is a key player of pancreatic alpha cell differentiation in zebrafish.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Divergent expression patterns of Sox9 duplicates in teleosts indicate a lineage specific subfunctionalization.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Two Cyp19 (P450 aromatase) genes on duplicated zebrafish chromosomes are expressed in ovary or brain.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

Evolution from fish to mammals by gene duplication

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5524304

31 August 2018

How Cichlids Diversify

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0180936

Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28738066

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Evolution of the tbx6/16 subfamily genes in vertebrates: insights from zebrafish

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28738066

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0180936

1 reference

5 September 2017

1 reference

5 September 2017

1 reference