Publications

Lab Publications

Here you can find a record of our research outputs, including work from exciting collaborations with groups around the world.

2026

Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom

Alice Laigle, Camille Cornet, Ashwini V. Mohan, Tobias Baril, Daniel Croll

openRxiv · 21 Jul 2026 · doi:10.64898/2026.07.21.739809

comparative genomics fungi structural variation transposable elements

Transposable elements underlie chromosomal fusions and fissions in a highly species-rich group of butterflies

Camille Cornet, Tobias Baril, Charlotte Wright, Kay Lucek

openRxiv · 17 Jun 2026 · doi:10.64898/2026.06.15.732387

transposable elements lepidoptera comparative genomics

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom

Tobias Baril, Daniel Croll

NAR Genomics and Bioinformatics · 05 Mar 2026 · 10.1093/nargab/lqag026

transposable elements fungi resources database github TE diversity and evolution

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus i Cenococcum Geophilum i Reveals Massive TE Expansion and RIP Defense Mechanism

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Benjamin Dauphin, Tobias Baril, Emmanuelle Morin, Ursula Oggenfuss, Stephanie Pfister, …, Igor V Grigoriev, Annegret Kohler, Francis Martin, Daniel Croll, Martina Peter

Genome Biology and Evolution · 22 Jan 2026 · doi:10.1093/gbe/evag017

fungi genome transposable elements

Evolution: Transposon traffic in the mycocosmos

Tobias Baril

Current Biology · 01 Jan 2026 · doi:10.1016/j.cub.2025.11.062

dispatch transposable elements fungi

2025

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen

Tobias Baril, Guido Puccetti, Daniel Croll

Nature Communications · 12 Nov 2025 · doi:10.1038/s41467-025-64944-4

transposable elements TE diversity and evolution population genomics fungi

Sub-lethal insecticide stress alters epimutation rate but not genetic mutation rate in the pest insect Myzus persicae

Benjamin J. Hunt, Kumar Saurabh Singh, Bartlomiej J. Troczka, Joanna Mackisack, Emma Randall, …, James Galbraith, Bram Kuijper, Ralf Nauen, Alex Hayward, Chris Bass

Insect Biochemistry and Molecular Biology · 01 Nov 2025 · doi:10.1016/j.ibmb.2025.104403

experimental evolution transposable elements arthropods resistance evolution

Genomic structure and life history variation of isofemale lineages of Myzus persicae with different levels of parasitization by Diaeretiella rapae

Mariane Possignolo Gomes, Ewerton Costa Lira, Idemauro Antonio Rodrigues de Lara, Rafael de Andrade Moral, Rita Rebollo, Tobias Baril, Fernando Luis Cônsoli

Scientific Reports · 10 Oct 2025 · doi:10.1038/s41598-025-19494-6

arthropods transposable elements resistance evolution

Hypermutator fungal pathogens: from threat to meltdown

Tobias Baril, Daniel Croll

Trends in Microbiology · 07 Aug 2025 · doi:10.1016/j.tim.2025.07.006

fungi transposable elements hypermutation opinion

2024

The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark i Scyliorhinus Canicula i Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates

The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark Scyliorhinus Canicula Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates

Hélène Mayeur, Jake Leyhr, John Mulley, Nicolas Leurs, Léo Michel, …, Tatjana Haitina, Kyle Martin, Sigrun I Korsching, Sylvie Mazan, Mélanie Debiais-Thibaud

Molecular Biology and Evolution · 01 Dec 2024 · doi:10.1093/MOLBEV/MSAE246

sharks genome transposable elements

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants

Caio A Leal-Dutra, Joel Vizueta, Tobias Baril, Pepijn W Kooij, Asta Rødsgaard-Jørgensen, Benjamin H Conlon, Daniel Croll, Jonathan Z Shik

Molecular Biology and Evolution · 17 Sep 2024 · doi:10.1093/molbev/msae197

fungi genome transposable elements domestication

Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline

Tobias Baril, James Galbraith, Alex Hayward

Molecular Biology and Evolution · 01 Apr 2024 · doi:10.1093/MOLBEV/MSAE068

transposable elements TE diversity and evolution resources software github annotation

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations

Gabriel David, Alicia Bertolotti, Ryan Layer, Douglas Scofield, Alexander Hayward, Tobias Baril, Hamish A Burnett, Erik Gudmunds, Henrik Jensen, Arild Husby

Genome Biology and Evolution · 15 Mar 2024 · doi:10.1093/GBE/EVAE049

birds structural variation resources

2023

A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici

Tobias Baril, Daniel Croll

BMC Research Notes · 16 Nov 2023 · doi:10.1186/S13104-023-06613-7

transposable elements resources database

Transposon accumulation at xenobiotic gene family loci in aphids

Tobias Baril, Adam Pym, Chris Bass, Alex Hayward

Genome Research · 01 Oct 2023 · doi:10.1101/gr.277820.123

comparative genomics transposable elements arthropods TE diversity and evolution

The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe

Ivy H. T. Lee, Wenyan Nong, Wai Lok So, Chris K. H. Cheung, Yichun Xie, …, Nathan Lo, Alexander Hayward, Ting Fung Chan, Hon-ming Lam, Jerome H. L. Hui

BMC Biology · 25 Sep 2023 · doi:10.1186/S12915-023-01703-1

genome lepidoptera transposable elements

A New Chromosome-Assigned Mongolian Gerbil Genome Allows Characterization of Complete Centromeres and a Fully Heterochromatic Chromosome

Thomas D Brekke, Alexander S T Papadopulos, Eva Julià, Oscar Fornas, Beiyuan Fu, …, Roberto de la Fuente, Jesus Page, Tobias Baril, Alexander Hayward, John F Mulley

Molecular Biology and Evolution · 01 May 2023 · doi:10.1093/MOLBEV/MSAD115

genome transposable elements mammals

2022

The genome sequence of the scarce swallowtail, i Iphiclides podalirius i

The genome sequence of the scarce swallowtail, Iphiclides podalirius

Alexander Mackintosh, Dominik R Laetsch, Tobias Baril, Sam Ebdon, Paul Jay, Roger Vila, Alex Hayward, Konrad Lohse

G3 Genes|Genomes|Genetics · 05 Aug 2022 · doi:10.1093/G3JOURNAL/JKAC193

genome lepidoptera transposable elements

Genome‐wide transcriptomic changes reveal the genetic pathways involved in insect migration

Toby Doyle, Eva Jimenez‐Guri, Will L. S. Hawkes, Richard Massy, Federica Mantica, …, Alex Hayward, Manuel Irimia, Jason W. Chapman, Chris Bass, Karl R. Wotton

Molecular Ecology · 12 Jul 2022 · doi:10.1111/MEC.16588

transcriptomics genome transposable elements arthropods

Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees

Sean T.S. Law, Wenyan Nong, Wai Lok So, Tobias Baril, Thomas Swale, …, Stephen S. Tobe, Zhen-Peng Kai, William G. Bendena, Alexander Hayward, Jerome H.L. Hui

Genomics · 01 Jul 2022 · doi:10.1016/j.ygeno.2022.110440

genome lepidoptera transposable elements

Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes

Wai Lok So, Wenyan Nong, Yichun Xie, Tobias Baril, Hai-yao Ma, …, Stephen S. Tobe, William G. Bendena, Zhen-peng Kai, Alexander Hayward, Jerome H. L. Hui

Nature Communications · 30 May 2022 · doi:10.1038/s41467-022-30690-0

genome arthropods comparative genomics transposable elements

The genome sequence of the lesser marbled fritillary, i Brenthis ino i , and evidence for a segregating neo-Z chromosome

The genome sequence of the lesser marbled fritillary, Brenthis ino , and evidence for a segregating neo-Z chromosome

Alexander Mackintosh, Dominik R Laetsch, Tobias Baril, Robert G Foster, Vlad Dincă, Roger Vila, Alexander Hayward, Konrad Lohse

G3 Genes|Genomes|Genetics · 28 Mar 2022 · doi:10.1093/g3journal/jkac069

genome lepidoptera transposable elements

Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus

Tobias Baril, Alexander Hayward

Mobile DNA · 16 Feb 2022 · doi:10.1186/s13100-022-00263-5

transposable elements lepidoptera TE diversity and evolution comparative genomics

Genome of the ramshorn snail Biomphalaria straminea—an obligate intermediate host of schistosomiasis

Wenyan Nong, Yifei Yu, Madeleine E Aase-Remedios, Yichun Xie, Wai Lok So, …, Xi Sun, Zhongdao Wu, Alexander Hayward, David E K Ferrier, Jerome H L Hui

GigaScience · 15 Feb 2022 · pmid:35166339

genome transposable elements molluscs

2021

The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775)

Alex Hayward, Roger Vila, Dominik R. Laetsch, Konrad Lohse, Tobias Baril

Wellcome Open Research · 10 Nov 2021 · doi:10.12688/wellcomeopenres.17280.1

genome lepidoptera transposable elements

Broadscale evolutionary analysis of eukaryotic DDE transposons

Mathilde Dupeyron, Tobias Baril, Alexander Hayward

openRxiv · 26 Sep 2021 · doi:10.1101/2021.09.26.461848

transposable elements TE diversity and evolution

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Wenyan Nong, Zhe Qu, Yiqian Li, Tom Barton-Owen, Annette Y. P. Wong, …, Stephen S. Tobe, William G. Bendena, Siu Gin Cheung, Alexander Hayward, Jerome H. L. Hui

Communications Biology · 19 Jan 2021 · doi:10.1038/S42003-020-01637-2

genome transposable elements arthropods

2020

Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)

Zhe Qu, Wenyan Nong, Yifei Yu, Tobias Baril, Ho Yin Yip, Alexander Hayward, Jerome H. L. Hui

BMC Genomics · 19 Oct 2020 · doi:10.1186/s12864-020-07145-1

genome transposable elements fish

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

Yiqian Li, Wenyan Nong, Tobias Baril, Ho Yin Yip, Thomas Swale, Alexander Hayward, David E. K. Ferrier, Jerome H. L. Hui

BMC Genomics · 15 Oct 2020 · doi:10.1186/s12864-020-07027-6

genome transposable elements molluscs

Millipede genomes reveal unique adaptations during myriapod evolution

Zhe Qu, Wenyan Nong, Wai Lok So, Tom Barton-Owen, Yiqian Li, …, Thomas Swale, Ting-Fung Chan, Alexander Hayward, Sai-Ming Ngai, Jerome H. L. Hui

PLOS Biology · 29 Sep 2020 · doi:10.1371/journal.pbio.3000636

genome transposable elements arthropods comparative genomics

Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

Mathilde Dupeyron, Tobias Baril, Chris Bass, Alexander Hayward

Mobile DNA · 29 Jun 2020 · doi:10.1186/s13100-020-00212-0

transposable elements TE diversity and evolution

Chromosomal level reference genome of the incense tree i Aquilaria sinensis i

Chromosomal‐level reference genome of the incense tree Aquilaria sinensis

Wenyan Nong, Sean T. S. Law, Annette Y. P. Wong, Tobias Baril, Thomas Swale, Lee Man Chu, Alexander Hayward, David T. W. Lau, Jerome H. L. Hui

Molecular Ecology Resources · 10 Mar 2020 · doi:10.1111/1755-0998.13154

genome transposable elements plants

A draft genome sequence of the elusive giant squid, i Architeuthis dux i

A draft genome sequence of the elusive giant squid, Architeuthis dux

Rute R da Fonseca, Alvarina Couto, Andre M Machado, Brona Brejova, Carolin B Albertin, …, Tomas Vinar, Blagoy Blagoev, Thomas Sicheritz-Ponten, Rasmus Nielsen, M Thomas P Gilbert

GigaScience · 16 Jan 2020 · doi:10.1093/gigascience/giz152

genome transposable elements molluscs