Biology subjects

Gerheim, C.

Publications and source records attributed to Gerheim, C..

6 recordsLinked to original sources

bioRxiv2026

Ontogenetic variation in composition and bioactivity of common adder (Vipera berus) venom revealed by genome-guided proteomics and in vitro functional assays

1Ontogenetic shifts in diet are well documented in snakes and are increasingly linked to age-related venom variation. The common adder, Vipera berus, exhibits a dietary transition from predominantly ectothermic prey in its early life to increasingly incorporating endothermic prey as an adult. Here, we investigate whether this dietary shift is reflected in age-related changes in the venom composition and bioactivity of V. berus. Venoms from captive-bred V. berus from Germany were obtained and pooled across five age groups, from neonates to adults. Venom profiles were assessed by SDS-PAGE and genome-guided shotgun proteomics, with quantification based on normalized spectral abundance factors (NSAF) using a toxin-gene catalogue generated from a novel V. berus genome assembly. In parallel, we assayed general protease and PLA2 activities, as well as FXa-, thrombin-, and plasmin-like activities, and cytotoxicity toward mammalian cell lines. We identified two distinct age-related venom phenotypes (ontotypes): an svMP/CTL-rich ontotype A ([≤]1 year) and an svSP/PLA2-rich ontotype B ([≥]2 years). Functionally, protease activity decreased with age, whereas thrombin-like, plasmin-like and PLA2 activities, and cytotoxicity, increased. Our findings indicate an ontogenetic shift in composition and activities of V. berus venom that parallels dietary transitions and potentially reflect adaptation to differing prey physiologies.

biochemistry↗

bioRxiv2025

A de novo reference genome of the golden jackal, Canis aureus

The golden jackal (Canis aureus) is rapidly expanding its range in Europe, driven by climate and habitat changes, human influence, and changes in competition with wolves. Its ecological flexibility enables it to thrive in various habitats, including urban areas, raising concerns about its potential role in spreading zoonotic diseases. Jackals may act as reservoirs for pathogens such as Lyme disease and babesiosis, affecting wildlife, humans, and pets. Their close genetic relationship with domestic dogs also increases the risk of hybridization and host-jumping, complicating disease dynamics. To better understand their dispersal ability and host-pathogen dynamics, we present the first chromosome-level genome assembly of the golden jackal, generated using PacBio HiFi sequencing and reference-based scaffolding. The final assembly has a total length of 2.53 Gb in 325 scaffolds, with 98.41% of the sequence anchored to the expected 38+XY chromosomes. The assembly shows high contiguity, with scaffold and contig N50 values of 68.03 Mb and 56.64 Mb, respectively. Annotation revealed 26,084 protein-coding genes, and repetitive elements account for 40.58% of the total assembly. This high-quality reference genome provides an essential resource for studying the genetic basis of the golden jackals adaptation, ecological interactions, and potential as a zoonotic reservoir. It also supports efforts to monitor population expansion and its effects on ecosystems. By advancing our understanding of golden jackal genetics, this work enables future research on evolution, host-pathogen dynamics, and the broader consequences of wildlife dispersal in a rapidly changing environment.

genomics↗

bioRxiv2024

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome

BackgroundThe time required for sequencing and de novo assembly of genomes is highly dependent on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow. As a result, genome projects are often not only limited by financial, computational and sequencing platform resources, but also delayed by second party sequencing service providers. By bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities and know-how, we aimed at generating a high-quality mammalian de novo genome in the shortest possible time period. Therefore, we streamlined all processes involved and chose a very fast dog as a model: The Whippet. FindingsWe present the first chromosome-level genome assembly of the Whippet. We used PacBio long-read HiFi sequencing and reference-guided scaffolding to generate a high-quality genome assembly. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. In addition, we used available mammalian genomes and transcriptome data to annotate the genome assembly. The annotation resulted in 28,383 transcripts resembling a total of 90.9% complete BUSCO genes and identified a repeat content of 36.5%. ConclusionsSequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week and adds a high-quality reference genome to the list of domestic dog breeds sequenced to date.

genomics↗

bioRxiv2024

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

BackgroundSequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data. ResultsIn this study, we present the chromosome-level genome assembly and annotation of the marine sacoglossan species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the Long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are 100-fold and 4-fold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa. We detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds. ConclusionsWe can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

genomics↗

bioRxiv2024

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

genomics↗

bioRxiv2024

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (Eliomys quercinus) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics datasets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome revealed a sharp population decline since the last interglacial, indicating an association between colder climates and population declines prior to anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conducted the first population genomic analysis for this species. We found clear evidence for population structure across the species core Central European range. Notably, our data shows that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through designation of ESUs.

genomics↗