(Q21559625)

English

Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae

scientific article

Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

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2 March 2020

Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae (English)

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2 March 2020

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De-Zhu Li

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De-Zhu

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Li

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2 March 2020

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Lei Zhao

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2 March 2020

Ning Zhang

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2 March 2020

Peng-Fei Ma

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Ma

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2 March 2020

Qi Liu

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2 March 2020

Zhen-Hua Guo

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Guo

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2 March 2020

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29 May 2013

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2 March 2020

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2 March 2020

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2 March 2020

e64642

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2 March 2020

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Creative Commons Attribution 4.0 International

29 May 2013

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HaMStR: profile hidden markov model based search for orthologs in ESTs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Meiosis specific coiled-coil proteins in Shizosaccharomyces pombe.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

The supermatrix approach to systematics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Selective elimination of messenger RNA prevents an incidence of untimely meiosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

A systematic search for positive selection in higher plants (Embryophytes)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

How much data are needed to resolve a difficult phylogeny?: case study in Lamiales.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Evolving disease resistance genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Recent highlights of RNA-polymerase-II-mediated transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Phylogeny estimation: traditional and Bayesian approaches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Utility of low-copy nuclear gene sequences in plant phylogenetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

RNA polymerase II: subunit structure and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

12 September 2017

Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

27 September 2017

Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

27 September 2017

A novel meiosis-specific protein of fission yeast, Meu13p, promotes homologous pairing independently of homologous recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

27 September 2017

DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE HEUCHERA GROUP (SAXIFRAGACEAE).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

30 May 2018

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

30 May 2018

Applications of next-generation sequencing in plant biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

30 May 2018

The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

30 May 2018

The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

30 May 2018

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

A Phylogeny of the Grass Family (Poaceae) Based on ndhF Sequence Data

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

The phylogeny of the BEP clade in grasses revisited: evidence from the whole-genome sequences of chloroplasts.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Chloroplast DNA and Biosystematics: The Effects of Intraspecific Diversity and Plastid Transmission

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Estimating species phylogenies using coalescence times among sequences.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Proteomic analysis of rice plasma membrane reveals proteins involved in early defense response to bacterial blight.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Increases in the number of SNARE genes parallels the rise of multicellularity among the green plants.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

An A/ENTH domain-containing protein functions as an adaptor for clathrin-coated vesicles on the growing cell plate in Arabidopsis root cells.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Expression profiling and bioinformatic analyses of a novel stress-regulated multispanning transmembrane protein family from cereals and Arabidopsis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Differential contributions of ribosomal protein genes to Arabidopsis thaliana leaf development.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Expression of genes encoding the rice translation initiation factor, eIF5A, is involved in developmental and environmental responses.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

The accuracy of species tree estimation under simulation: a comparison of methods

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Arabidopsis plasma membrane proteomics identifies components of transport, signal transduction and membrane trafficking.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

The novel gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 of rice encodes a putative coiled-coil protein required for homologous chromosome pairing in meiosis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

The age of the grasses and clusters of origins of C4photosynthesis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Evolutionary History of the Grasses

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3667173

29 November 2018

Multiple Sequence Alignment Accuracy and Phylogenetic Inference

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

21 January 2018

Characterization of plant eukaryotic translation initiation factor 6 (eIF6) genes: The essential role in embryogenesis and their differential expression in Arabidopsis and rice

1 reference

https://pubmed.ncbi.nlm.nih.gov/23734211

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses

1 reference

https://pubmed.ncbi.nlm.nih.gov/23734211

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/23734211

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence and expression analysis of the C3HC4-type RING finger gene family in rice

1 reference

https://pubmed.ncbi.nlm.nih.gov/23734211

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Salt stress alleviation in transgenic Vigna mungo L. Hepper (blackgram) by overexpression of the glyoxalase I gene using a novel Cestrum yellow leaf curling virus (CmYLCV) promoter

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

7 January 2021

based on heuristic

inferred from DOI database lookup

Gene Trees in Species Trees

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

7 January 2021

based on heuristic

inferred from DOI database lookup

Phylogeny and Subfamilial Classification of the Grasses (Poaceae)

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

7 January 2021

based on heuristic

inferred from DOI database lookup

comparing De Novo Transcriptome Assemblers Using Illumina RNA-Seq Reads

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0064642

7 January 2021

based on heuristic

inferred from DOI database lookup

Identifiers

10.1371/JOURNAL.PONE.0064642

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23734211%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

2013PLoSO...864642Z

0 references

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23734211%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23734211%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

ResearchGate publication ID

0 references

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