Kentaro K. Shimizu

Highly recommended EMBO Workshop on Plant Photobiology (ISPP2026) in Les Diablerets, Switzerland! (even if I may be slightly biased...) Registration open. We are very much looking forward to seeing you there! ⬇️

Purifying selection on deleterious variants affected by the combination of subgenomes and gene expression in bread wheat Halstead-Nussloch et al. quantify genome-wide purifying selection on deleterious variants using high-quality annotation of 10 genomes of bread wheat. Strong purifying selection is observed in the cate...

Our new publication from the 10+ Wheat Genome Project in Cell Reports! The combined effect of #polyploidy and expression on selection will inform the target of future #wheat breeding to mitigate the effect of deleterious variants. By a former PhD Gwyn and a postdoc Moeko
www.cell.com/cell-reports...

Our new publication on HOBIT, a software tool for polyploid gene expression analysis. Compared with our previous method HomeoRoq (2014), HOBIT enables direct and higher-quality analysis of complex allohexaploid species such as bread wheat.

Press release in English about the new paper in Nature Communications thanks to the Earlham Institute doi.org/10.1038/s414...

Interviewed by Nikkei Science (Japanese edition of Scientific American). The photo shows a Swiss Alps village where a new species, Cardamine insueta, formed in the past 150 years via hybridization and genome duplication. The article also covers wheat and Arabidopsis kamchatica.

現在進行中の進化を野外で研究する 学生時代、山で出合った植物、ミヤマハタザオ。シロイヌナズナに似ているが形態も分布も違う。この植物を使えば、現在進行中の進化を検証できるのではないか。そうひらめいた清水健太郎（現・チューリヒ大学教授）は、分子生物学を野外の植物の研究に適用し、進化ゲノム学を推し進めてきた。

Excited to be featured in Nature Digest’s “Japanese Author” series! They wrote about some of my work in Nature and sister journals. #genome #evolution #wheat #linguistics #polyploidy #biodiversity #Darwin
Article (Japanese): doi.org/10.1038/ndig...

Capturing language change through the genes - NCCR Evolving Language When populations meet, they typically exchange genes. Their languages meet too, and such encounters can change languages. But how much do languages actually change through contact, and do these change...

📰When populations meet, they exchange genes, but also language features. According to a new study by NCCR researchers, contact between human populations increases the resemblance between their languages to similar extents all over the world, but differently.

evolvinglanguage.ch/capturing-la...

Patterns of genetic admixture reveal similar rates of borrowing across diverse scenarios of language contact Human population contact leads to consistently similar rates of linguistic borrowing, but effects vary across linguistic features.

New paper out in Science Advances!
We studied language & genetic evolution using the GeLaTo database—focusing on burrowing and schismogenesis.
Link: doi.org/10.1126/scia...

Special thanks to @chiarabarbieri.bsky.social @annagraff.bsky.social @balthasarbickel.bsky.social @nccrlanguage.bsky.social

A moderated statistical test for detecting shifts in homeolog expression ratios in allopolyploids Allopolyploids arise through hybridization between related species, carrying multiple sets of chromosomes from distinct progenitor, referred to as subgenomes. Within allopolyploids, duplicated genes a...

Our new preprint introduces HOBIT, a bioinformatics tool for allopolyploid RNA-seq. It’s directly applicable to allohexaploid species like bread wheat and outperforms our previous method, HomeoRoq, in 2014.
Software: github.com/bitdessin/he... by Jianqiang
Preprint: www.biorxiv.org/content/10.1...

My first thesis chapter is out 🎉!
doi.org/10.1007/s001...

We discovered two potentially novel yellow rust resistance loci in a new Asian wheat NAM population and gained insights into their distribution.

Time to celebrate with my first publication cake🍰!
@kkshimizu1.bsky.social @cimmyt.bsky.social

Press release: Preserving #biodiversity within the crop species wheat is valuable for food security. Thanks to collaborators, particularly the partnership with Kyoto University, my alma mater.
doi.org/10.1007/s001... @kajung.bsky.social‬
www.news.uzh.ch/en/articles/... in English and in German

Unveiling yellow rust resistance in the near-Himalayan region: insights from a nested association mapping study - Theoretical and Applied Genetics Key message This study identified two potentially novel yellow rust resistance loci in traditional Asian wheat varieties and gives insights into the distribution of resistances in high disease-pressur...

New publication on #wheat disease resistance by my group member Kathi Jung (PhD in Science and Policy)! Using the genome assembly of the Japanese cultivar Norin 61, she identified yellow rust resistance loci in landraces from the Himalayan region.
doi.org/10.1007/s001...
@kajung.bsky.social

The emergence of eukaryotes as an evolutionary algorithmic phase transition | PNAS The origin of eukaryotes represents one of the most significant events in evolution since it allowed the posterior emergence of multicellular organ...

A fundamental and groundbreaking study by Jordi Bascompte, a colleague from our department:

The emergence of eukaryotes as an evolutionary algorithmic phase transition | PNAS www.pnas.org/doi/10.1073/...

A major milestone on global biodiversity by our colleague, the Florian Altermatt group — just published in Nature.

Perspectives on mating–system evolution: comparing concepts in plants and animals Abstract. The study of mating systems, defined as the distribution of who mates with whom and how often in a sexually reproducing population, forms a core

I am so happy to see this review online finally! A lot of work, but a lot of fun too! Thank you to all the co-authors! @gretabocedi.bsky.social @trinebilde.bsky.social @jevbio.bsky.social

academic.oup.com/jeb/advance-...

Congratulations to Kathi on successfully defending her PhD! 🎉🎓 As the tradition, her PhD hat made by the lab members showcases her fascinating research on Asian wheat cultivars. Well done, Kathi! 🌾👏

Natural neopolyploids: a stimulus for novel research Recently formed allopolyploid species offer unprecedented insights into the early stages of polyploid evolution. This review examines seven well-studied neopolyploids (we use ‘neopolyploid’ to refer ...

Our review of recently evolved allopolyploid plants is out. It was very nice writing this paper with great colleagues! We dedicate this paper to the memory of Richard Abbott who contributed so much to this and many other topics in plant evolution. doi.org/10.1111/nph....

Natural neopolyploids: a stimulus for novel research Recently formed allopolyploid species offer unprecedented insights into the early stages of polyploid evolution. This review examines seven well-studied neopolyploids (we use ‘neopolyploid’ to refer ...

A new review, published on Valentine's Day! We explore the future of the study of contemporary polyploid speciation such as Cardamine insueta in Switzerland, building on discussions from the Polyploidy 2023 conference led by Doug & Pam Soltis, Patrick @nicrodemo.bsky.social doi.org/10.1111/nph.20437

Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures ABSTRACT. Common wheat is allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3ʹ RNA-seq, is a t

A new paper online! Improved GO annotation of the bread wheat genome will be useful, thanks to the first author Yasuyuki and the last author Atsushi. The homeolog expression was studied using 25 Asian cultivars including Norin 61. @plantcellphysiol.bsky.social doi.org/10.1093/pcp/...

UZH: Postdoc in population genomics The NCCR Evolving Language invites applications for a Postdoctoral Researcher in population genomics to study the demography of humans and domesticated crop species related to language evolution at the Department of Evolutionary Biology and Environmental Studies, University of Zurich.

The Shimizu group seeks a Postdoctoral Researcher in population genomics at the University of Zurich to study genetic and language evolution. Applications are open now. More info: https://jobs.uzh.ch/job-vacancies/postdoc-in-population-genomics/40227b73-2360-4e79-8924-844e5f5ed4c0 #postdoc

Excited to be an invited speaker at the CSH Asia 'Plant Reproductive Development and Genomics' conference on Awaji Island, Japan, May 18-22, 2025! 🌸 Awaji Island is home to beautiful botanical gardens, a legacy of the Flower Expo 2000. More details: www.csh-asia.org?content/2653

A new open postdoc position in population genomics! Reposting appreciated. Demography of human beings and crop plants. Attached is a group picture during a lab retreat in Lichtenstein. Job description:
jobs.uzh.ch/job-vacancie...
@nccrlanguage.bsky.social