List of works - Kentaro K. Shimizu

A stigmatic gene confers interspecies incompatibility in the Brassicaceae

scientific article published on 01 July 2019

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

scientific article published on 17 July 2021

Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana

scientific article published on 08 June 2020

Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica

scientific article published on 14 October 2017

Allopolyploid origin of Cardamine asarifolia (Brassicaceae): incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene

scientific article published on 9 March 2006

Attractive and repulsive interactions between female and male gametophytes in Arabidopsis pollen tube guidance

scientific article published on 01 October 2000

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

scientific article published on 16 June 2015

Cell type-specific transcriptome of Brassicaceae stigmatic papilla cells from a combination of laser microdissection and RNA sequencing

scientific article

Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches.

scientific article

Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica.

scientific article published on 12 July 2016

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes

scientific article published on 27 November 2020

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

scientific article published on 21 January 2022

Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection.

scientific article

Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility

scientific article published in 2023

Double-Locking Mechanism of Self-Compatibility in Arabidopsis thaliana: The Synergistic Effect of Transcriptional Depression and Disruption of Coding Region in the Male Specificity Gene

scientific article published on 11 September 2020

Duplicated pollen-pistil recognition loci control intraspecific unilateral incompatibility in Brassica rapa

scientific article published on 26 June 2017

Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility.

scientific article

Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing

scientific article

Efficient purging of deleterious mutations in plants with haploid selfing

scientific article

Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

scientific article (publication date: 11 January 2017)

Evolution and control of imprinted FWA genes in the genus Arabidopsis

scientific article

Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

scientific article published on 18 April 2010

Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae).

scientific article published on 3 June 2015

Evolutionary and ecological genomics of Arabidopsis.

scientific article

Experimental and Field Data Support Range Expansion in an Allopolyploid Arabidopsis Owing to Parental Legacy of Heavy Metal Hyperaccumulation

scientific article published on 30 September 2020

Exploring deep-time relationships between cultural and genetic evolution in Northeast Asia: Supporting Information

article

Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae).

scientific article

Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

scientific article published on 22 November 2020

Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia

scientific article

Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity

article

Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology.

scientific article

Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations.

scientific article

Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering inArabidopsis thaliana

scientific article published in 2023

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

scientific article

Genomics meets remote sensing in global change studies: monitoring and predicting phenology, evolution and biodiversity

scientific article published in December 2017

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

scientific article published on 11 January 2016

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes

scientific article published in 2011

Integrative research efforts at the boundary of biodiversity and global change research

Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri.

scientific article

Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus

scientific article (publication date: 2013)

Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought-responsive genes.

scientific article

Metal accumulation and its effect on leaf herbivory in an allopolyploid species Arabidopsis kamchatica inherited from a diploid hyperaccumulator <scp>A. halleri</scp>

scientific article published in 2020

Molecular basis of flowering under natural long-day conditions in Arabidopsis

scientific article published on 24 September 2018

Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes

scientific article published on 03 September 2021

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

scientific article

Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy

scientific article published on 26 February 2014

Multiple wheat genomes reveal global variation in modern breeding

scientific article published on 25 November 2020

Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory

scientific article published in 2021

Nitrogen as a key regulator of flowering in Fagus crenata: understanding the physiological mechanism of masting by gene expression analysis

scientific article published on 07 August 2014

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

scientific article published in Nature Communications

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes.

scientific article published on 29 June 2016

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

scientific article (publication date: September 2011)

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

article

Polyploidy before and after domestication of crop species

scientific article published in 2022

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

scientific article

Positional bias in variant calls against draft reference assemblies.

scientific article

Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica

scientific article (publication date: 2012)

Reference-guided de novo assembly approach improves genome reconstruction for related species.

scientific article

Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment

scientific article

Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?

scientific article published in 2022

Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss

scientific article

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.

scientific article published on 18 July 2016

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity.

scientific article published on 31 October 2016

The Nagoya Protocol could backfire on the Global South

scientific article published on 14 May 2018

The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri

scientific article published on 15 September 2009

The more the merrier: recent hybridization and polyploidy in cardamine.

scientific article published on 30 September 2013

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae).

scientific article published on 18 January 2017

The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

scientific article (publication date: 7 February 2012)

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

scientific article published on 14 July 2013

Transcriptional characteristics and differences in Arabidopsis stigmatic papilla cells pre- and post-pollination

scientific article published on 19 December 2014

Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence

scientific article published on 05 November 2019

Using a two-stage convolutional neural network to rapidly identify tiny herbivorous beetles in the field

scientific article published in 2021

Using knockout mutants to reveal the growth costs of defensive traits.

scientific article published on 26 January 2011

Utility of commercial high‐resolution satellite imagery for monitoring general flowering in Sarawak, Borneo

scientific article published in 2023

List of works by Kentaro K. Shimizu

A stigmatic gene confers interspecies incompatibility in the Brassicaceae

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana

Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica

Allopolyploid origin of Cardamine asarifolia (Brassicaceae): incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene

Attractive and repulsive interactions between female and male gametophytes in Arabidopsis pollen tube guidance

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

Cell type-specific transcriptome of Brassicaceae stigmatic papilla cells from a combination of laser microdissection and RNA sequencing

Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches.

Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica.

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection.

Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility

Double-Locking Mechanism of Self-Compatibility in Arabidopsis thaliana: The Synergistic Effect of Transcriptional Depression and Disruption of Coding Region in the Male Specificity Gene

Duplicated pollen-pistil recognition loci control intraspecific unilateral incompatibility in Brassica rapa

Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility.

Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing

Efficient purging of deleterious mutations in plants with haploid selfing

Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Evolution and control of imprinted FWA genes in the genus Arabidopsis

Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae).

Evolutionary and ecological genomics of Arabidopsis.

Experimental and Field Data Support Range Expansion in an Allopolyploid Arabidopsis Owing to Parental Legacy of Heavy Metal Hyperaccumulation

Exploring deep-time relationships between cultural and genetic evolution in Northeast Asia: Supporting Information

Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae).

Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia

Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity

Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology.

Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations.

Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in<i>Arabidopsis thaliana</i>

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

Genomics meets remote sensing in global change studies: monitoring and predicting phenology, evolution and biodiversity

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes

Integrative research efforts at the boundary of biodiversity and global change research

Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri.

Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus

Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought-responsive genes.

Metal accumulation and its effect on leaf herbivory in an allopolyploid species <i>Arabidopsis kamchatica</i> inherited from a diploid hyperaccumulator <scp><i>A. halleri</i></scp>

Molecular basis of flowering under natural long-day conditions in Arabidopsis

Multiple Wheat Genomes Reveal Novel <i>Gli-2</i> Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy

Multiple wheat genomes reveal global variation in modern breeding

Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory

Nitrogen as a key regulator of flowering in Fagus crenata: understanding the physiological mechanism of masting by gene expression analysis

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes.

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

Polyploidy before and after domestication of crop species

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

Positional bias in variant calls against draft reference assemblies.

Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica

Reference-guided de novo assembly approach improves genome reconstruction for related species.

Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment

Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?

Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity.

The Nagoya Protocol could backfire on the Global South

The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri

The more the merrier: recent hybridization and polyploidy in cardamine.

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae).

The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

Transcriptional characteristics and differences in Arabidopsis stigmatic papilla cells pre- and post-pollination

Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence

Using a two-stage convolutional neural network to rapidly identify tiny herbivorous beetles in the field

Using knockout mutants to reveal the growth costs of defensive traits.

Utility of commercial high‐resolution satellite imagery for monitoring general flowering in Sarawak, Borneo