Biology subjects

Greve, C.

Publications and source records attributed to Greve, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrated genomics and transcriptomics reveal mechanisms of extreme dietary adaptation in vampire bats

Vampire bats are the only tetrapods that feed exclusively on blood. To uncover the molecular basis of this extreme dietary specialization, we generated six new reference genomes, including genomes of all three vampire bat species, and integrated comparative analyses of gene sequence evolution (selection signatures, duplications, and losses) with transcriptomic data from six major organs to identify shifts in gene expression. Our integrative analyses reveal sequence or expression changes in 150 genes that illuminate the genetic mechanisms underlying sanguivory. Through comparative analyses and experiments, we show that the enlarged vampire bat stomach has increased connective tissue content enabling extreme expansion, is pH-neutral, and exhibits reduced mucus production, together providing molecular insights into its shift from a digestive to an absorptive organ for water, electrolytes, and vitamins. We further uncover pathway-level molecular changes underlying altered gastrointestinal motility; trypsin-dependent protein digestion; upregulated amino acid catabolism with key aspects diverging from other mammals; impaired dietary fat digestion counterbalanced by increased fatty acid synthesis; defective sugar metabolism and natural insulin deficiency; enhanced heme iron absorption; and adult splenic erythropoiesis. Together, these findings reveal the molecular adaptations that enable one of the most extreme dietary transitions among vertebrates.

evolutionary biology↗

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↗

bioRxiv2026

Genome-wide identification of heat shock proteins (HSP70) in the Cuban painted snail Polymita picta: evolutionary constraints face climate change challenges

Climate change poses a critical threat for biodiversity. Among ectothermal animals, terrestrial molluscs are considered highly vulnerable to temperature increase and drought due to their low vagility and specialized ecological requirements. In response to thermal stress, heat shock proteins (HSP70) play a crucial role in the response syndrome and phenotypic plasticity and mediate the adaptation to fluctuating environments. Here, we performed the first genome-wide identification and characterization of the HSP70 family in a Neotropical terrestrial gastropod of high conservation concern: the Cuban painted snail Polymita picta. Using comprehensive bioinformatic approaches, we identified HSP70 paralogs, analysed their structural features and assessed sequence variation, highlighting their potential relevance for thermoresistance. Our findings reveal an HSP70 repertoire of ten diversified sequences with signatures of functional specialization and possible adaptive variation linked to environmental temperature regimes. Using novel molecular resources, this pioneering analysis establishes a baseline for early warning systems, integrating stress-related biomarkers into conservation management and climate change adaptation strategies for threatened terrestrial molluscs.

genomics↗

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↗

bioRxiv2025

A Prelude to Conservation Genomics: First Chromosome-Level Genome Assembly of a Flying Squirrel (Pteromyini: Pteromys volans)

The Siberian flying squirrel (Pteromys volans) represents the only European Pteromyini species. Thus, it is biogeographically unique due to its specialised anatomy and biology as a volant rodent. As a result of habitat fragmentation and destruction, Siberian flying squirrels experience severe and ongoing population declines throughout most of their distribution. While considered Least Concern throughout their immense Eurasian distribution, this species is red-listed as Vulnerable and even Critically Endangered in parts of its range. More knowledge about the population structure and overall biology is needed to improve conservation efforts for this umbrella and flagship species of old-growth boreal forests. Here, we present the first chromosome-level genome assembly of any Pteromyini, represented by P. volans (Uoulu_pteVol_1.0). The final assembly has a total length of 2.85 Gbp in 19 chromosome-scale scaffolds with only minor differences in the chromosomal structure compared to other Sciuridae. All chromosome-scale scaffolds show indications for telomeres at both ends; the N50 value and busco as well as k-mer completeness scores are high with 157.39 Mbp and 97 - 99 %, respectively, indicating chromosome-level quality of the assembly. Based on whole-genome data from 17 rodent species, P. volans clusters according to known evolutionary relationships. Additionally, we present a new 16,511 bp long mitogenome unveiling differences from known conspecific mitogenomes. We propose the utility of the new reference genome for further research and development of conservation-applied genetic methods.

genomics↗

bioRxiv2025

Sequencing a botanical monument: a chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.) at the Botanical Garden of the University of Padua (Italy)

The rapid decline in global biodiversity highlights the urgent need for conservation efforts, with botanical gardens playing a crucial role in ex situ plant preservation. Monumental plants, such as the 400-year-old Goethes Palm (Chamaerops humilis L.) at the UNESCO Botanical Garden of the University of Padua (Italy), serve as vital flagship species with significant ecological and cultural value. In this study, we present the first high-quality, chromosome-level genome assembly of C. humilis, using PacBio HiFi and Arima Hi-C sequencing technologies. This genome is the most contiguous and complete within the Arecaceae family to date, with an exceptionally high repeat content of 88%, of which 63% is attributed to Long Terminal Repeat (LTR) elements. Comparative analysis of the transposable element (TE) landscape in palms suggests that the LTR expansion in C. humilis is likely the result of recent TE bursts. Furthermore, we provide the first comprehensive annotation of microRNAs (miRNAs) in the Arecaceae family, identifying, for the first time in palms, the miRNA family miR827, which plays a key role in nutrient regulation. Microsatellite analysis suggests that it probably belongs to the Western genetic lineage of C. humilis. These findings represent a significant advancement in the conservation genomics of this species, laying the groundwork for enhanced preservation strategies, with botanical gardens as pivotal actors in the fight to safeguard global biodiversity.

genomics↗

bioRxiv2024

Genome of the enigmatic watering-pot shell reveals adaptations of a living suction anchor

The watering pot shells have been rightly called "the weirdest bivalves" for their highly modified body plan and fused tubular shell that resemble the spout of a watering can. This adventitious tube has defied rational explanation as an adaptive pathway and yet arose twice convergently. We present the first genome for the clade Anomalodesmata: an annotated chromosome-scale genome of Verpa penis (Linnaeus, 1758). The first watering pot shell ever described ranges across southeast Asia but is nonetheless extremely rare and has never previously been sequenced. The assembly length of 507 Mb, with a contig N50 of 5.33 Mb, has 96.5% of sequences anchored onto 19 pseudochromosomes. Contrary to expectations from such a highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral condition of heterodont bivalves (1N=19). A new hypothesis based on analysis of the living animals and literature explains the adaptive significance of this body form: it is structurally optimised for vertical stability in soft sediments, with parallels to engineering principles of a suction anchor. Our study offers new insights to a long-standing mystery in molluscan body forms, and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.

evolutionary biology↗

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

Rearrangements and accelerated mutation rates on Dendrodorididae mitogenomes rumble their evolution

The systematics of the family Dendrodorididae poses a challenge to evolutionary biologists, as their mitochondrial and nuclear markers provide contradictory phylogenetic signals. Nuclear pseudogenes or exogenous contamination are hypothesized to cause the molecular discordance. However, these hypotheses have not been tested. We used genomic data from seven Dendrodorididae species to investigate the evolution of this family. Two mitogenomes displayed a novel structural rearrangement in nudibranchs, involving the translocation of three collinear genes and five surrounding tRNAs. Additionally, we found numerous mitogenomic regions with non-synonymous mutations and multiple indels in both coding and ribosomal genes. Protein modeling resulted in similar structures, suggesting that functionality is conserved. Phylogenies using mitogenomic data confirmed a specific clade membership for the rearranged mitogenomes. The incorporation of nuclear data did not fully resolve the systematic relationships of Dendrodorididae, acknowledging the evolutionary complexity of this group. The present study provides novel evidence on sudden molecular changes in mitogenomes, and highlights the relevance of using genomic data to unveil rare evolutionary processes, which is critical for understanding evolution of neglected taxa.

evolutionary biology↗

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

De Novo Genome assembly of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invadingthe River Rhine

The Caucasian dwarf goby Knipowitschia cf. caucasica is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality chromosome-scale reference genome of Knipowitschia cf. caucasica by combining PacBio, Omni-C and Illumina technologies. The size of the assembled genome is 956.58 Mb with a N50 scaffold length of 43 Mb, which includes 92.3 % complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. 98.96 % of the assembly sequence was assigned to 23 chromosome-level scaffolds, with a GC-content of 42.83 %. Repetitive elements account for 53.08 % of the genome. The chromosome-level genome contained 26,404 transcripts with 23,210 multi-exons, of which 26,260 genes were functionally annotated. In summary, the high-quality genome assembly provides a fundamental basis to understand the adaptive advantage of the species.

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↗

bioRxiv2022

A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)

The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.

genomics↗

bioRxiv2022

High quality genomes corroborate 29 chromosomes of the haploid Hyles (Lepidoptera: Sphingidae) karyotype

BackgroundMorphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics. ResultsThe genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function. ConclusionsOur two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).

genomics↗

bioRxiv2021

Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding

Feeding exclusively on blood, vampire bats represent the only obligate sanguivorous lineage among mammals. To uncover genomic changes associated with adaptations to this unique dietary specialization, we generated a new haplotype-resolved reference-quality genome of the common vampire bat (Desmodus rotundus) and screened 26 bat species for genes that were specifically lost in the vampire bat lineage. We discovered previously-unknown gene losses that relate to metabolic and physiological changes, such as reduced insulin secretion (FFAR1, SLC30A8), limited glycogen stores (PPP1R3E), and a distinct gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2, CTRL) and distinct pathogen diversity of blood (RNASE7). Interestingly, the loss of REP15 likely helped vampire bats to adapt to high dietary iron levels by enhancing iron excretion and the loss of the 24S-hydroxycholesterol metabolizing enzyme CYP39A1 could contribute to their exceptional cognitive abilities. Finally, losses of key cone phototransduction genes (PDE6H, PDE6C) suggest that these strictly-nocturnal bats completely lack cone-based vision. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to sanguivory.

evolutionary biology↗

bioRxiv2020

Biodiversity genomics of small metazoans: high quality de novo genomes from single specimens of field-collected and ethanol-preserved springtails

Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in evolutionary sciences, ecology, systematics and in biodiversity-related applied fields such as environmental management and natural product research. Advances in DNA sequencing technologies make genome sequencing feasible for many non-genetic model species. However, genome sequencing today relies on large quantities of high quality, high molecular weight (HMW) DNA which is mostly obtained from fresh tissues. This is problematic for biodiversity genomics of Metazoa as most species are small and yield minute amounts of DNA. Furthermore, briging living specimens to the lab bench not realistic for the majority of species. Here we overcome those difficulties by sequencing two species of springtails (Collembola) from single specimens preserved in ethanol. We used a newly developed, genome-wide amplification-based protocol to generate PacBio libraries for HiFi long-read sequencing. The assembled genomes were highly continuous. They can be considered complete as we recovered over 95% of BUSCOs. Genome-wide amplification does not seem to bias genome recovery. Presence of almost complete copies of the mitochondrial genome in the nuclear genome were pitfalls for automatic assemblers. The genomes fit well into an existing phylogeny of springtails. A neotype is designated for one of the species, blending genome sequencing and creation of taxonomic references. Our study shows that it is possible to obtain high quality genomes from small, field-preserved sub-millimeter metazoans, thus making their vast diversity accessible to the fields of genomics.

genomics↗

bioRxiv2020

How old are dragonflies and damselflies? Odonata (Insecta) transcriptomics resolve familial relationships

Dragonflies and damselflies, representing the insect order Odonata, are among the earliest flying insects with living (extant) representatives. However, unravelling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, an issue particularly prevalent in damselfly families and fossil lineages. Here we present the first transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all of the orders families (except Austropetaliidae and Neopetaliidae). All damselfly families and most dragonfly families are recovered as monophyletic groups. Our Molecular clock estimates suggest that crown-Zygoptera (damselflies) and -Anisoptera (dragonflies) both arose during the late Triassic. Several of the observed long inner branches in our topology are indicative of the extinction of once flourishing lineages. We also find that exophytic egg laying behaviour with a reduced ovipositor evolved in certain dragonflies during the late Jurassic / early Cretaceous. Lastly, we find that certain fossils have an unexpected deterring impact in divergence dating analysis.

evolutionary biology↗