Biology subjects

De Panis, D.

Publications and source records attributed to De Panis, D..

6 recordsLinked to original sources

bioRxiv2025

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

BackgroundReference genomes for the entire sea turtle clade have the potential to reveal the genetic basis of traits driving the ecological and phenotypic diversity in these ancient and iconic marine species. Furthermore, these genomic resources can support conservation efforts and deepen our understanding of their unique evolution. ResultsWe present haplotype-resolved, chromosome-level reference genomes and high-quality gene annotations for five sea turtle species. This completes the catalog of reference genomes of the entire sea turtle clade when combined with our previously published reference genomes. Our analysis reveals remarkable genome synteny and collinearity across all species, despite the clades origin dating back more than 60 million years. Regions of high interspecific genetic distance and intraspecific genetic diversity are consistently clustered in genomic hotspots, which are enriched with genes coding for immune response proteins, olfactory receptors, zinc fingers, and G-protein-coupled receptors. These hotspot regions may offer insights into the genetic mechanisms driving phenotypic divergence among species, and represent areas of significant adaptive potential. Ancient demographic analysis revealed a synchronous population expansion among sea turtle species during the Pleistocene, with varying magnitudes of demographic change, likely shaped by their diverse ecological adaptations, and biogeographic contexts. ConclusionsOur work provides genomic resources for exploring genetic diversity, evolutionary adaptations, and demographic histories of sea turtles. We outline genomic regions with increased diversity, linked to immune response, sensory evolution, and adaptation to varying environments that have historically been subject to strong diversifying selection, and likely will underpin sea turtles responses to future environmental change. These reference genomes can assist conservation by providing insights into the demographic and evolutionary processes that sustain and threaten these iconic species.

genomics↗

bioRxiv2025

ERGA-BGE Reference Genome of Phyllidia flava (Nudibranchia: Phyllidiidae), a Relict Species Endemic to the Mediterranean Sea

Phyllidia flava, the only Mediterranean representative of the otherwise Indo-Pacific family Phyllididae, is a radula-less dorid nudibranch that feeds exclusively on toxic sponges, from which it derives defensive and camouflage compounds. Although not currently listed as endangered, this relict species remains vulnerable due to its restricted distribution and the rising temperatures of the Mediterranean Sea. A total of 13 contiguous chromosomal pseudomolecules were assembled, resulting in a chromosome-level genome spanning 1.9 Gb. This assembly comprises 2,032 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.4 Mb and 169.7 Mb, respectively. This reference genome will serve as a valuable resource for conservation efforts, provide a robust calibration point for studying nudibranch phylogenetics based on the Tethys Ocean closure, and lay the groundwork for research into toxic prey diet specialisation.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of the Striped Field Mouse (Apodemus agrarius), a Widespread and Abundant Species in Central and Eastern Europe

The reference genome of Apodemus agrarius provides a valuable resource for phylogenetic studies of rodents, particularly mice, and for understanding factors that influence the geographical distribution of the species across East Asia and East Europe. A total of 25 contiguous chromosomal pseudomolecules were assembled from the genome sequence (23 autosomes and 2 sex chromosomes). This chromosome-level assembly encompasses 2.6 Gb, composed of 242 contigs and 60 scaffolds, with contig and scaffold N50 values of 35 Mb and 119 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions

The reference genome of Gluvia dorsalis is the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.

genomics↗

bioRxiv2024

ERGA-BGE Reference Genome of the Northern chamois (Rupicapra rupicapra): Europe's most abundant mountain ungulate

The reference genome of Rupicapra rupicapra (subsp. rupicapra) provides insights into the genetic makeup that enabled this iconic mountain ungulate to adapt to its harsh environment, including its ability to survive in extreme weather and high altitudes--factors that are increasingly important in the face of climate change. A total of 29 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.62 Gb, composed of 124 contigs and 76 scaffolds, with contig and scaffold N50 values of 77 Mb and 101 Mb, respectively.

genomics↗

bioRxiv2023

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗