PXD074775-1

PXD074775 is an original dataset announced via ProteomeXchange.

Title	Genomic exaptation and regulatory landscape shifts as key mechanisms enabling flatworm terrestrialization
Description	Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering the evolutionary origins of land biodiversity. Yet, the genomic basis of the physiological and metabolic adaptations required for life on land remains poorly understood across most terrestrial animal phyla. Planarians (Platyhelminthes) offer a powerful model, as only one terrestrial lineage, the Geoplanidae (order Tricladida), is known. Here, we integrated genomics, transcriptomics, and proteomics to explore the genetic changes potentially supporting terrestrial adaptation. We identified a major burst of gene gain in the lineage leading to Tricladida, preceding the radiation of terrestrial planarians. Upon abiotic stress exposure, terrestrial and freshwater species exhibited distinct responses: most differentially expressed genes belonged to orthogroups gained in Tricladida, with over half under strong directional selection in terrestrial flatworms, suggesting their adaptive relevance. Transcriptomic profiles revealed divergent strategies: terrestrial species upregulated ancient genes, while freshwater species downregulated a separate set of ancestral genes. Across all datasets, the abiotic stress response toolkit in terrestrial planarians was markedly different from freshwater relatives, with significant regulatory divergence. Our results highlight gene gain and co-option, rather than lineage-specific innovations, as key drivers of terrestrial flatworm evolution, emphasizing genomic exaptation and regulatory shifts as central to terrestrialization in Platyhelminthes. This study provides the first genome-wide view of the genetic basis of flatworm terrestrialization and sheds light on broader patterns of animal terrestrial adaptation.
HostingRepository	PRIDE
AnnounceDate	2026-04-06
AnnouncementXML	Submission_2026-04-05_16:10:47.689.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Schmidtea mediterranea (Freshwater planarian flatworm); NCBI TaxID: NEWT:79327; scientific name: Obama nungara; NCBI TaxID: NEWT:1826298;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-24 11:22:00	ID requested
⏵ 1	2026-04-05 16:10:48	announced

Carbonetto B, Ben, í, tez-, Á, lvarez L, Garc, í, a-Vernet R, Eleftheriadi K, Vargas-Ch, á, vez C, Escudero N, Salces-Ortiz J, Rojo I, Fern, á, ndez-, Á, lvarez F Á, Alwell C, Chiva C, Sabid, ó E, Mateos E, Carbayo F, Fern, á, ndez R, Genomic Exaptation and Regulatory Landscape Shifts as Key Mechanisms Enabling Flatworm Terrestrialization. Genome Biol Evol, 18(3):(2026) [pubmed]

10.1093/gbe/evag063;

submitter keyword: planarians, evolution, flatworm,terrestrialization

Rosa Fernández
contact affiliation	Metazoa Phylogenomics & Genome Evolution Lab, Institute of Evolutionary Biology (CSIC-UPF). Passeig Marítim de la Barceloneta 37-49; 08003 Barcelona; Spain
contact email	rmfernandezgarcia00@gmail.com
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/2026/04/PXD074775

PRIDE project URI

• PRIDE
  1. PXD074775
     1. Label: PRIDE project
     2. Name: Genomic exaptation and regulatory landscape shifts as key mechanisms enabling flatworm terrestrialization