Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids

@article{baudement2026developmental,
  title = {{Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids}},
  author = {Marie-Odile Baudement and Diego Perojil Morata and Gareth Gillard and Pooran Dewari and Manu Kumar Gundappa and Tomasz Podgorniak and Lars Grønvold and Damir Baranasic and Audrey Laurent and François Giudicelli and Bojan Zunar and Erika Carrera-García and Aline Perquis and Aurélien Brionne and Tan Thi Nguyen and Rose Ruiz Daniels and Gabriela Merino and David Thybert and Garth Ilsley and Alexandra Louis and Torgeir Hvidsten and Camille Berthelot and Peter Harrison and Hugues Roest Crollius and Yann Guiguen and Boris Lenhard and Simen Sandve and Julien Bobe and Matthew Kent and Sigbjørn Lien and Daniel Macqueen},
  journal = {Nature Ecology \& Evolution},
  year = {2026},
  month = oct,
  doi = {10.1038/s41559-026-03171-6},
  url = {https://hal.inrae.fr/hal-05794833v1},
  note = {CC BY},
}

TY  - JOUR
TI  - Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids
AU  - Marie-Odile Baudement
AU  - Diego Perojil Morata
AU  - Gareth Gillard
AU  - Pooran Dewari
AU  - Manu Kumar Gundappa
AU  - Tomasz Podgorniak
AU  - Lars Grønvold
AU  - Damir Baranasic
AU  - Audrey Laurent
AU  - François Giudicelli
AU  - Bojan Zunar
AU  - Erika Carrera-García
AU  - Aline Perquis
AU  - Aurélien Brionne
AU  - Tan Thi Nguyen
AU  - Rose Ruiz Daniels
AU  - Gabriela Merino
AU  - David Thybert
AU  - Garth Ilsley
AU  - Alexandra Louis
AU  - Torgeir Hvidsten
AU  - Camille Berthelot
AU  - Peter Harrison
AU  - Hugues Roest Crollius
AU  - Yann Guiguen
AU  - Boris Lenhard
AU  - Simen Sandve
AU  - Julien Bobe
AU  - Matthew Kent
AU  - Sigbjørn Lien
AU  - Daniel Macqueen
PY  - 2026
DA  - 2026/10/12
JO  - Nature Ecology & Evolution
DO  - 10.1038/s41559-026-03171-6
UR  - https://hal.inrae.fr/hal-05794833v1
AB  - Whole genome duplication (WGD) events during early vertebrate evolution may have promoted phenotypic innovation by expanding the genetic material for functional diversification. However, their ancient origins obscure how gene regulation evolved during rediploidization, the process that generates duplicate genes and regulatory elements following WGD. Salmonids provide a unique window to these mechanisms, because they experienced a more recent autotetraploid WGD and remain at an earlier stage of rediploidization. Here we generated 771 multiomics datasets spanning embryonic and adult tissues in Atlantic salmon and rainbow trout to investigate the evolution of gene expression and regulatory elements. Our analyses show that regulatory evolution following the salmonid WGD was shaped by developmental and tissue-specific constraints known to act across vertebrate species. We identify a peak of within-genome regulatory constraint at the vertebrate phylotypic period, associated with the functional retention of duplicated enhancer pairs harbouring deeply conserved non-coding elements enriched in motifs for master developmental transcription factors. We further identify roles for enhancers and transposable elements in the expression divergence of duplicated genes. This study advances the understanding of regulatory evolution following WGD and offers an open resource supporting vertebrate comparative genomics and research applications in salmonid aquaculture and conservation.
SN  - 2397-334X
ER  -