PXD064337

PXD064337 is an original dataset announced via ProteomeXchange.

Title	Lack of a universal genomic toolkit for animal terrestrialisation
Description	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.
HostingRepository	PRIDE
AnnounceDate	2026-06-15
AnnouncementXML	Submission_2026-06-15_08:15:38.343.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Phorcus turbinatus; NCBI TaxID: NEWT:43341; scientific name: Eisenia fetida; NCBI TaxID: NEWT:6396; scientific name: Ligia oceanica; NCBI TaxID: NEWT:96856; scientific name: Litoditis marina; NCBI TaxID: NEWT:1654675; scientific name: Porcellio scaber; NCBI TaxID: NEWT:64697; scientific name: Caenorhabditis elegans; NCBI TaxID: NEWT:6239; scientific name: Physella; NCBI TaxID: NEWT:175859; scientific name: Theba pisana; NCBI TaxID: NEWT:145622; scientific name: Leptonemertes chalicophora; NCBI TaxID: NEWT:980089; scientific name: Ooperipatellus viridimaculatus; NCBI TaxID: NEWT:123606; scientific name: Siphonaria pectinata; NCBI TaxID: NEWT:57642; scientific name: Schmidtea mediterranea (Freshwater planarian flatworm); NCBI TaxID: NEWT:79327; scientific name: Lineus sanguineus; NCBI TaxID: NEWT:187800; scientific name: Arenicola marina; NCBI TaxID: NEWT:6344; scientific name: Obama nungara; NCBI TaxID: NEWT:1826298; scientific name: Hirudo medicinalis; NCBI TaxID: NEWT:6421;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-27 09:18:41	ID requested
⏵ 1	2026-06-15 08:15:38	announced

Dataset with its publication pending

submitter keyword: proteomics,terrestrialization

Rosa Fernández
contact affiliation	Metazoa Phylogenomics & Genome Evolution Lab, Institute of Evolutionary Biology (CSIC-UPF)
contact email	rosa.fernandez@ibe.upf-csic.es
lab head
Cristina Chiva
contact affiliation	University Pompeu Fabra
contact email	cristina.chiva@upf.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064337

PRIDE project URI

• PRIDE
  1. PXD064337
     1. Label: PRIDE project
     2. Name: Lack of a universal genomic toolkit for animal terrestrialisation