Dataset Information

Lack of a universal genomic toolkit for animal terrestrialisation

ABSTRACT: Animal terrestrialisation, the transition from aquatic to land environments, is one of the most impactful events in animal evolution, having occurred independently across several phyla. Yet, whether these transitions relied on a conserved genomic toolkit remains unexplored. To address this gap, we integrated large-scale comparative genomics and machine learning from close to 1,000 animal genomes with experimentally induced abiotic stress responses, transcriptomics, and proteomics across diverse aquatic and terrestrial invertebrates. Here, we show that no universal genetic toolkit underlies animal terrestrialisation. Instead, species-specific gene coexpression networks inferred from stress experiments, mimicking key selective pressures related to life on land (e.g., exposure to UV-B light, osmotic stress, and different oxygen availability), revealed hub genes that were largely unique to each lineage. Despite this divergence, independent lineages co-opted distinct sets of ancient gene families, most predating terrestrial life, resulting in functionally convergent genomic responses. This pattern was congruent with phylogenomic analyses, which indicated that most gene families originated early in animal evolution, with limited gene gain and extensive gene loss associated with the emergence of terrestrial lineages. Machine learning identified a small set of gene families predictive of habitat type, enriched in stress-related functions such as cytochrome P450 metabolism and vitamins A and E. Many of these also functioned as hub genes in the coexpression networks, linking them to key positions in species-specific regulatory architectures. These findings challenge the notion of a shared terrestrialisation program and instead reveal a model of functional convergence through lineage-specific genomic repurposing of ancient genes.

INSTRUMENT(S):

ORGANISM(S): Ligia Oceanica Siphonaria Pectinata Schmidtea Mediterranea (freshwater Planarian Flatworm) Leptonemertes Chalicophora Caenorhabditis Elegans Phorcus Turbinatus Physella Hirudo Medicinalis Lineus Sanguineus Ooperipatellus Viridimaculatus Obama Nungara Porcellio Scaber Theba Pisana Arenicola Marina Litoditis Marina Eisenia Fetida

TISSUE(S): Multicellular Organism

SUBMITTER: Cristina Chiva

LAB HEAD: Rosa Fernández

PROVIDER: PXD064337 | Pride | 2026-06-15

REPOSITORIES: Pride

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			Action	DRS
	2023MQ065_RQGA_001_01_1ug.raw	Raw
	2023MQ065_RQGA_002_01_1ug.raw	Raw
	2023MQ065_RQGA_003_01_1ug.raw	Raw
	2023MQ065_RQGA_TPIS-S1-S3-DB-2501.pdResult	Other
	2023MQ066_RQGA_001_01_1ug.raw	Raw

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Publications

Convergent genomic trajectories shape adaptation to life on land across animal lineages.

Martínez-Redondo Gemma I GI Eleftheriadi Klara K Salces-Ortiz Judit J Escudero Nuria N Fernández-Álvarez Fernando Ángel FÁ Carbonetto Belén B Vargas-Chávez Carlos C García-Vernet Raquel R Palma-Guerrero Javier J Rentería Libe L Rojo Iñaki I Chiva Cristina C Sabidó Eduard E Bombarely Aureliano A Fernández Rosa R

Nature communications 20260718

How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared genomic mechanisms underlie these transitions. Here, we combine large-scale comparative genomics, machine learning, and multi-omics data, including proteomics and transcriptomics from stress experiments relevant to terrestrial environmental challenges in 17 species, to investigate the genomic basis of ...[more]

PMID: 42471324

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