Biology subjects

Boehne, A.

Publications and source records attributed to Boehne, A..

10 recordsLinked to original sources

bioRxiv2026

ERGA-BGE reference genomes of Hyalomma lusitanicum and its obligate Francisella endosymbiont as a genomic resource for One Health research

Hyalomma lusitanicum is a characteristic tick species of the western Mediterranean region, with a well-established distribution across the Iberian Peninsula. It is strongly associated with wild ungulates, particularly red deer, as well as livestock, to which it can transmit a wide range of pathogens, including viruses, bacteria, and protozoa. Here, we present three genomic resources for H. lusitanicum: a scaffold-scale nuclear genome, the complete mitochondrial genome, and the complete genome of its associated Francisella bacterial endosymbiont. The nuclear genome assembly spans 1.81 Gb and comprises 59 scaffolds, with a scaffold N50 of 153.6 Mb (L50 = 5) and no gaps, indicating high contiguity and completeness with a gene annotation completeness BUSCO score of 97.1 %. Genome annotation of the nuclear assembly identified 20,638 protein-coding genes, 1,422 non-coding genes, and 5,775 pseudogenes. A total of 18 scaffolds were assembled as putative chromosomes, exceeding the 11 chromosomes inferred as ancestral; however, synteny analyses suggest that several scaffolds likely represent fragmented portions of the same chromosome, probably due to incomplete Hi-C scaffolding. Despite this, the assembly represents one of the most complete tick nuclear genomes generated to date. In addition, we report the complete genome of a Francisella endosymbiont (1.51 Mb, 1,679 genes), characterized by a high proportion of pseudogenes and reduced genome size, consistent with patterns of genome reduction associated with obligate symbiosis. Together, these genomic resources provide a framework to investigate local adaptation and host-symbiont evolution, and to support improved surveillance, control, and management strategies for species of public health relevance.

genomics↗

bioRxiv2025

Multiple instances of river-lake introgression in the adaptive radiation of sailfin silversides in Wallace's Dreampond

While adaptive radiations significantly contribute to the worlds biodiversity, much is unknown about the genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate the speciation process by generating genetic diversity on which diversifying selection can act. Sailfin silverside fishes (Telmatherinidae) in the Malili Lakes system in Sulawesi have diversified within the last 2 million years. We assembled and annotated a chromosome-scale reference genome of the riverine sailfin silverside Telmatherina bonti and generated whole genome sequences of all species of Telmatherina in Lake Matano, South Sulawesi, Indonesia, one of the worlds oldest and deepest lakes. We reconstructed the phylogenetic relationships within the adaptive radiation of sailfin silversides and inferred past and ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins and roundfins. However, within clades, we found mismatches between morphology-based taxonomic assignments and genome-wide genetic relationships. We found signs of both old and ongoing introgression between river-dwelling T. bonti and the lacustrine sharpfin group, as shown in elevated D-statistic, f4-ratio and f-branch statistic. Levels of excess allele sharing between riverine species and the three most common lacustrine species declined with increasing distance from the river-inlet, indicating ongoing introgression at the lake-river interface. This combination of past and ongoing hybridisation in a radiating species flock makes Lake Matano Telmatherina a particularly valuable system to study fundamental mechanisms driving rapid speciation under genomic exchange. The phylogenomic framework elaborated in this study provides the foundation for studies of the processes shaping this charismatic radiation.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Coenonympha oedippus: an IUCN endangered European butterfly species occurring in two ecotypes

The reference genome of the False ringlet (Coenonympha oedippus) will serve as a valuable resource for uncovering the genetic mechanism underlying the species' adaptability to two ecologically distinct habitats. Through this genome we might be able to determine whether (i) each ecotype is monophyletic, indicating that the ecological divergence represents an early stage of speciation, (ii) the ecotypes have evolved through divergent evolution of habitat preference, or (iii) the differences between ecotypes are solely due to phenotypic plasticity or epigenetic variation. This reference genome is also a prerequisite for the planning, design, and implementation of conservation measures for this endangered species, taking into account its intraspecific diversity. Furthermore, it holds broader implications for population genomic studies of the species-rich genus Coenonympha, which includes some of the most endangered butterfly taxa in Europe. The complete genome sequence was assembled into 30 contiguous chromosomal pseudomolecules (sex chromosomes included). This chromosome-level assembly encompasses 0.39 Gb, composed of 385 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.8 Mb and 14.2 Mb, respectively.

genomics↗

bioRxiv2025

A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species

BackgroundReference genomes have a wide range of applications. Yet, we are from a complete genomic picture for the tree of life. We here contribute another piece to the puzzle by providing a high-quality reference genome for the Ural Owl (Strix uralensis), a species of conservation concern and efforts affected by habitat destruction and climate change. ResultsWe generated a reference genome assembly for the Ural Owl based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. It figures amongst the best avian genome assemblies currently available (BUSCO completeness of 99.94 %). The primary assembly had a size of 1.38 Gb with a scaffold N50 of 90.1 Mb, while the alternative assembly had a size of 1.3 Gb and a scaffold N50 of 17.0 Mb. We show an exceptionally high repeat content (21.07 %) that is different from those of other bird taxa with repeat extensions. We confirm a Strix characteristic chromosomal fusion and support the observation that bird microchromosomes have a higher density of genes, associated with a reduction in gene length due to shorter introns. An analysis of gene content provides evidence of changes in the keratin gene repertoire as well as modifications of metabolism genes of owls. This opens an avenue of research if this is related to flight adaptations. The population size history of the Ural Owl decreased over long periods of time with increases during the Eemian interglacial and stable size during the last glacial period. Ever since it is declining to its currently lowest effective population size. We also investigated cell culture of progressive passages as a tool for genetic resources. Karyotyping of passages confirmed no large variants, while a SNP analysis revealed a low presence of short variants across cell passages. ConclusionsThe established reference genome is a valuable resource for ongoing conservation efforts, but also for (avian) comparative genomics research. Further research is needed to determine whether cell culture passages can be safely used in genomic research.

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↗

bioRxiv2023

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae - Phoxinus phoxinus) provide evidence of haplotype diversity

AO_SCPLOWBSTRACTC_SCPLOWIn this study we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C). We achieved a haploid size of 940 Megabase pairs (Mbp) for haplome one and 929 Mbp for haplome two with high scaffold N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, respectively, indicating a highly complete genome assembly. We detected notable heterozygosity (1.43%) and a high repeat content (approximately 54%), primarily consisting of DNA transposons, which contribute to genome rearrangements and variations. We found substantial structural variations within the genome, including insertions, deletions, inversions, and translocations. These variations affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, and stress response. In the annotation of protein-coding genes, 30,980 mRNAs and 23,497 protein-coding genes were identified with a high completeness score, which further underpins the high contiguity of our genome assemblies. We performed a gene family evolution analysis by comparing our proteome to ten other teleost species, which identified immune system gene families that prioritise histone-based disease prevention over NLR-based immune responses. Additionally, demographic analysis indicates historical fluctuations in the effective population size of P. phoxinus, likely correlating with past climatic changes. This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus Phoxinus and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterised by high heterozygosity.

genomics↗

bioRxiv2023

Sexual antagonism and sex determination in three syngnathid species alongside male pregnancy gradient and varying sex roles.

The allocation of energy towards gamete production, parental care, mate choice, sex roles, and sexual dimorphism generates divergence in selection pressures between the sexes, leading to opposing fitness strategies and sexual antagonism (SA). Due to the shared genetic makeup, a single genomic locus can contain a gene or allele with differing fitness impacts on each sex. This intralocus sexual conflict can be resolved via intersex bias in gene expression and/or formation of sex-linked genomic regions, that may also regulate sex determination. Sex determination (SD) encompasses environmental SD (ESD), monogenic SD, and polygenic SD. Occasionally, shifts from one SD locus to another can occur. While the precise mechanisms driving these shifts are unknown, SA is believed to be a major contributor. To investigate the link between SA and SD, we selected three syngnathid species along the gradient of male pregnancy that evolved with different sex roles and intensities of sexual dimorphism. By looking at intersex genetic divergence (Fst) and sex-biased expression patterns, we uncovered that sex role and mate competition, rather than male pregnancy, primarily drive SA. Furthermore, we identified processes related to non-coding RNAs and biased allele expression as mediators of SA. Most notably, we discovered intraspecies sex chromosome polymorphism in Hippocampus erectus. Overall, we report important details on the interplay between SA and SD, and suggest that understanding SA and its resolution mechanisms is crucial for unraveling the evolution of SD in diverse species.

evolutionary biology↗

bioRxiv2023

Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europes eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGAs pan- European network. To demonstrate the communitys capability and capacity to realise ERGAs ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGAs member base. SSP aims to aid participating researchers through i) establishing standards for and collecting of sample/ specimen metadata; ii) prioritisation of species for genome sequencing; and iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGAs high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

genomics↗

bioRxiv2022

Contribution of hybridization to the evolution of a derived reproductive strategy in ricefishes

Transitions between reproductive strategies are costly and involve major changes in life history, behaviour and morphology. Nevertheless, in Sulawesi ricefishes, pelvic-brooding evolved from transfer-brooding in two distantly related lineages within in the genera Adrianichthys and in Oryzias, respectively. Females of pelvic-brooding species carry their eggs attached to their belly until the fry hatches. Despite their phylogenetic distance, both pelvic-brooding lineages share a set of external morphological traits. A recent study found no direct gene-flow between pelvic-brooding lineages suggesting independent evolution of the derived reproductive strategy. It could, however, also be more complex. Pre-existing variation in an admixed population may enable the re-use of genetic variants when subjected to similar external selection pressure, resulting in similar phenotypes. We thus used a multi-species coalescent (MSC) model and D-statistics to identify gene-tree - species-tree incongruencies, to evaluate the evolution of pelvic-brooding with respect to inter-specific gene-flow not only between pelvic-brooding lineages, but between pelvic-brooding lineages and other Sulawesi ricefish lineages. We found a general network-like evolution in Sulawesi ricefishes and as previously reported, no gene-flow between the pelvic-brooding lineages. Instead, we found hybridization between the ancestor of pelvic-brooding Oryzias and the common ancestor of the four Oryzias species from Lake Poso, home of the pelvic-brooding Adrianichthys lineage. Further, indications of introgression were located within two confidence intervals of quantitative trait loci (QTL) associated with pelvic-brooding in O. eversi. We thus hypothesize that a mix of de novo mutations and (ancient) standing genetic variation shaped the evolution of pelvic-brooding. Significance statementThe evolution of pelvic-brooding in Oryzias eversi (Beloniformes:Adrianichthyidae), was recently described to be independent from another pelvic-brooding ricefish lineage (Adrianichthys) from Sulawesi. We confirmed these results, and detected no gene flow between the two distantly related pelvic-brooding lineages. Instead, we found ancient gene flow from another Orzyias lineage into the pelvic-brooding Oryzias lineage. One of the previously described QTL for pelvic brooding overlaps with a region of high introgression signal. Therefore, we assume that not only de novo mutations contributed to the evolution of pelvic-brooding in Orzyias, but that introduced ancient genetic variation was likely also recruited for the evolution of this derived brooding strategy.

evolutionary biology↗

bioRxiv2020

Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes

Sex is a fundamental trait that is determined, depending on the species, by different environmental and/or genetic factors, including various types of sex chromosomes. While the functioning and emergence of sex chromosomes have been explored in species scattered across the eukaryotic tree of life, little is known about tempo and mode of sex chromosome evolution in closely related species. Here, we examine the dynamics of sex chromosome evolution in an archetypical example of adaptive radiation, the cichlid fishes of African Lake Tanganyika. Through inspection of male and female genomes from 244 cichlid taxa and the analysis of transcriptomes from 66 taxa, we identify signatures of sex chromosomes in 79 taxa, involving 12 different linkage groups. We estimate that Tanganyikan cichlids have the highest rates of sex chromosome turnover and heterogamety transitions known to date. We further show that the recruitment of chromosomes as sex chromosomes is not at random and that some chromosomes have convergently emerged as sex chromosomes in cichlids, which provides empirical support to the "limited options" hypothesis of sex chromosome evolution.

evolutionary biology↗