List of works - Atsushi Toyoda

A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

scientific article published on 07 October 2021

A key metabolic gene for recurrent freshwater colonization and radiation in fishes

scientific article published on 01 May 2019

A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization

scientific article published on 28 October 2019

An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3

scientific article published in Scientific Reports

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

scientific article published on 25 August 2020

Anisogamy evolved with a reduced sex-determining region in volvocine green algae

scientific article published on 08 March 2018

Arms race between anti‐silencing and <scp>RdDM</scp> in noncoding regions of transposable elements

scientific article published in 2023

Assembling the genome of the African wild rice by exploiting synteny in closely related species

article

Author Correction: RNA interference-independent reprogramming of DNA methylation in Arabidopsis

scientific article published on 16 December 2020

CRISPR/Cas9-based knockouts reveal that CpRLP1 is a negative regulator of the sex pheromone PR-IP in the Closterium peracerosum-strigosum-littorale complex.

scientific article published on 19 December 2017

Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes

scientific article published on 08 January 2020

Chromosomal-level Genome Assembly of the Coffee Bee Hawk Moth Reveals the Evolution of Chromosomes and the Molecular Basis of Distinct Phenotypes

scientific article published in 2023

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

scientific article published on 15 January 2021

Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori

scientific article published on 18 February 2019

Controlling gene activation by enhancers through a drug-inducible topological insulator

scientific article published on 05 May 2020

Correction: A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization

scientific article published on 19 June 2020

Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing

scientific article published on 08 July 2019

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

scientific article published on 26 June 2019

Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice

scientific article published on 09 May 2022

Endoribonuclease ENDU-2 regulates multiple traits including cold tolerance via cell autonomous and nonautonomous controls in Caenorhabditis elegans.

scientific article

Enhancer adoption caused by genomic insertion elicits interdigital Shh expression and syndactyly in mouse

scientific article published on 18 December 2017

Ethylene signaling mediates host invasion by parasitic plants ⬇️

scientific article published on 28 October 2020

Evolution of sequence-specific anti-silencing systems in Arabidopsis.

scientific article published on 18 December 2017

Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes

scientific article published on 01 March 2021

Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation

scientific article published on 31 May 2021

Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits.

scientific article

Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita

scientific article published on 15 September 2017

Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae

scientific article published in 2022

Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna

scientific article published on 30 April 2024

Insights into the genomic evolution of insects from cricket genomes

scientific article published on 14 June 2021

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication ⬇️

scientific article published on 27 May 2020

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community

scientific article published in Nature Communications

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

scientific article published on 06 June 2019

Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic.

scientific article published on 29 May 2018

Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut

scientific article published on 01 June 2020

Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

scientific article published on 12 April 2019

RNA interference-independent reprogramming of DNA methylation in Arabidopsis

scientific article published on 30 November 2020

Reduction in chromosome mobility accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans

scientific article

Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles

scientific article published in Nature Communications

Reply to Renner: Meticulous investigation, not sequencing effort, leads to robust conclusion

scientific article published on 29 September 2020

The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19

scientific article published in 2021

The prehistoric peopling of Southeast Asia

scientific article

Time-course transcriptomics analysis reveals key responses of submerged deepwater rice to flooding

scientific article published on 23 February 2018

Unique H2-utilizing lithotrophy in serpentinite-hosted systems

scientific article published in 2022

List of works by Atsushi Toyoda

A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

A key metabolic gene for recurrent freshwater colonization and radiation in fishes

A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization

An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Anisogamy evolved with a reduced sex-determining region in volvocine green algae

Arms race between anti‐silencing and <scp>RdDM</scp> in noncoding regions of transposable elements

Assembling the genome of the African wild rice by exploiting synteny in closely related species

Author Correction: RNA interference-independent reprogramming of DNA methylation in Arabidopsis

CRISPR/Cas9-based knockouts reveal that CpRLP1 is a negative regulator of the sex pheromone PR-IP in the Closterium peracerosum-strigosum-littorale complex.

Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes

Chromosomal-level Genome Assembly of the Coffee Bee Hawk Moth Reveals the Evolution of Chromosomes and the Molecular Basis of Distinct Phenotypes

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori

Controlling gene activation by enhancers through a drug-inducible topological insulator

Correction: A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization

Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice

Endoribonuclease ENDU-2 regulates multiple traits including cold tolerance via cell autonomous and nonautonomous controls in Caenorhabditis elegans.

Enhancer adoption caused by genomic insertion elicits interdigital Shh expression and syndactyly in mouse

Ethylene signaling mediates host invasion by parasitic plants ⬇️

Evolution of sequence-specific anti-silencing systems in Arabidopsis.

Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes

Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation

Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits.

Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita

Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae

Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna

Insights into the genomic evolution of insects from cricket genomes

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication ⬇️

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic.

Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut

Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

RNA interference-independent reprogramming of DNA methylation in Arabidopsis

Reduction in chromosome mobility accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans

Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles

Reply to Renner: Meticulous investigation, not sequencing effort, leads to robust conclusion

The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19

The prehistoric peopling of Southeast Asia

Time-course transcriptomics analysis reveals key responses of submerged deepwater rice to flooding

Unique H2-utilizing lithotrophy in serpentinite-hosted systems