Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants (Q21283927)

19 August 2022

Bing Liu

2

Bing

Liu

1 reference

19 August 2022

Lujun Yu

3

Lujun

Yu

1 reference

19 August 2022

Dongru Feng

4

Dongru

Feng

1 reference

19 August 2022

Hongbin Wang

5

Hongbin

Wang

1 reference

19 August 2022

Jinfa Wang

6

Jinfa

Wang

1 reference

Crystal structure of 12-oxophytodienoate reductase 3 from tomato: self-inhibition by dimerization

19 August 2022

language of work or name

English

0 references

publication date

2009

0 references

published in

BMC Evolutionary Biology

0 references

volume

9

0 references

issue

1

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page(s)

90

0 references

cites work

1 reference

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PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

19 March 2017

1 reference

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The jasmonate signal pathway

19 March 2017

1 reference

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The probability of preservation of a newly arisen gene duplicate

19 March 2017

1 reference

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Initial sequencing and analysis of the human genome

19 March 2017

1 reference

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12-Oxophytodienoate-10,11-reductase: occurrence of two isoenzymes of different specificity against stereoisomers of 12-oxophytodienoic acid

19 March 2017

1 reference

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

19 March 2017

1 reference

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Clustal W and Clustal X version 2.0

19 March 2017

1 reference

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PAML 4: phylogenetic analysis by maximum likelihood

19 March 2017

1 reference

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ProtTest: selection of best-fit models of protein evolution

19 March 2017

1 reference

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MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

19 March 2017

1 reference

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

19 March 2017

1 reference

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The evolutionary fate and consequences of duplicate genes

19 March 2017

1 reference

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Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

19 March 2017

1 reference

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SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

19 March 2017

1 reference

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The rapid generation of mutation data matrices from protein sequences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Identification of the OsOPR7 gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Polyploidy and genome evolution in plants

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

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

19 March 2017

1 reference

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Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

19 March 2017

1 reference

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Characterization and cDNA-microarray expression analysis of 12-oxophytodienoate reductases reveals differential roles for octadecanoid biosynthesis in the local versus the systemic wound response

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

The Arabidopsis male-sterile mutant, opr3, lacks the 12-oxophytodienoic acid reductase required for jasmonate synthesis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

12-Oxophytodienoate reductase 3 (OPR3) is the isoenzyme involved in jasmonate biosynthesis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Molecular cloning and characterization of 12-oxophytodienoate reductase, an enzyme of the octadecanoid signaling pathway from Arabidopsis thaliana. Structural and functional relationship to yeast old yellow enzyme

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Molecular evidence for an ancient duplication of the entire yeast 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=2688005

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=2688005

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

The probability of duplicate gene preservation by subfunctionalization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

An evolutionary trace method defines binding surfaces common to protein families

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Intron gain and loss in segmentally duplicated genes in rice

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Jasmonate biochemical pathway

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Duplication events and the evolution of segmental identity

12 September 2017

1 reference

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mRNA-mediated intron losses: evidence from extraordinarily large exons

12 September 2017

1 reference

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

The pattern of intron loss

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Rice octadecanoid pathway

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Structure and expression of 12-oxophytodienoate reductase (subgroup I) genes in pea, and characterization of the oxidoreductase activities of their recombinant products.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Functional divergence in protein (family) sequence evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cells.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

12 September 2017

The jasmonate pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Enzymes of the biosynthesis of octadecanoid-derived signalling molecules

12 September 2017

1 reference

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A homolog of old yellow enzyme in tomato. Spectral properties and substrate specificity of the recombinant protein.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Octadecanoid and hexadecanoid signalling in plant defence

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Phylogenetic analysis using PHYLIP.

12 September 2017

1 reference

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Intron loss and gain during evolution of the catalase gene family in angiosperms

12 September 2017

1 reference

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Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss

12 September 2017

1 reference

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The octadecanoic pathway: signal molecules for the regulation of secondary pathways

12 September 2017

1 reference

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Jasmonic acid signalling and herbivore resistance traits constrain regrowth after herbivore attack in Nicotiana attenuata

12 September 2017

1 reference

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The arabidopsis DELAYED DEHISCENCE1 gene encodes an enzyme in the jasmonic acid synthesis pathway

30 May 2018

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30 May 2018

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On the incidence of intron loss and gain in paralogous gene families.

29 November 2018

1 reference

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Nematode small subunit phylogeny correlates with alignment parameters

29 November 2018

1 reference

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Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana.

29 November 2018

1 reference

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A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences.

29 November 2018

1 reference

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Genomic analysis of the 12-oxo-phytodienoic acid reductase gene family of Zea mays

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Evidence that human genes of modular proteins have retained significantly more ancestral introns than their fly or worm orthologues

29 November 2018

1 reference

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Genomic background predicts the fate of duplicated genes: evidence from the yeast genome

29 November 2018

1 reference

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Diverse environmental cues transiently regulate OsOPR1 of the “octadecanoid pathway” revealing its importance in rice defense/stress and development

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Evidence that rice and other cereals are ancient aneuploids

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Frequent intron loss in the white gene: a cautionary tale for phylogeneticists.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Maximum-likelihood approach for gene family evolution under functional divergence.

29 November 2018

1 reference

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Structure and regulation of OPR1 and OPR2, two closely related genes encoding 12-oxophytodienoic acid-10,11-reductases from Arabidopsis thaliana

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688005

Statistical methods for testing functional divergence after gene duplication

29 November 2018

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12 December 2020

Polyploidy: recurrent formation and genome evolution

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12 December 2020

The fate of duplicated genes: loss or new function?

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12 December 2020

Multiple Sequence Alignment Accuracy and Phylogenetic Inference

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12 December 2020

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

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12 December 2020

The evolution of single-copy Drosophila nuclear 4f-rnp genes: spliceosomal intron losses create polymorphic alleles

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12 December 2020

Identifiers

DOI

10.1186/1471-2148-9-90

0 references