Biology subjects

Winter, S.

Publications and source records attributed to Winter, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Fertilization offsets the maternal age effect on mouse oocytes provided the oviduct is not itself aged

Advanced maternal age compromises oocyte quality, and it is widely assumed that these deficits are transmitted to embryos. However, because most studies rely on in vivo conception, it has been difficult to separate the effects of oocyte aging from those of an aged fertilization environment. In aging mice, we observed that the fraction of ovulated oocytes forming implantation sites after in vivo conception fell ~3.7-fold, raising the question of whether this was due to reduced fertilization, reduced embryo quality or reduced support from the aged reproductive tract. Therefore we fertilized oocytes of aged and young mice in vitro with a shared young-donor sperm preparation, holding the fertilization environment constant and removing paternal variability. Hallmarks of maternal age were largely offset following fertilization in vitro: aged oocytes produced blastocysts at rates comparable to young controls, with altered - but not deficient - cell-lineage composition and no detectable impairment in development to term (E18.5) after transfer to young oviducts. Proteomic analysis revealed that, unlike the transcriptomic signature, the proteomic age signature of oocytes was not faithfully propagated to the blastocyst: for a subset of proteins, particularly those depleted in aged oocytes, the direction of the age effect reversed between oocyte and blastocyst. Comparison with parthenogenetically activated oocytes showed this divergence to be fertilization-dependent, implicating fertilization - rather than mere embryonic cleavage - as the driver of proteomic change. Stable-isotope labelling in live embryos showed that blastocysts from aged, fertilized oocytes both synthesized more new protein and retained less maternal protein than young counterparts; neither effect was detectable after parthenogenesis. Puromycin labelling, by contrast, showed a maternal-age-associated rise in bulk synthesis regardless of route. Together, these results indicate that the maternal-age effect on the oocyte proteome is labile rather than fixed and can be offset by fertilization itself, provided the maternal environment is not itself aged.

developmental biology↗

bioRxiv2026

Chromosome-level reference genome assembly of the Saimaa ringed seal (Pusa saimensis) - an ancient glacial relict landlocked pinniped

We present a high-quality chromosome-level reference genome for the Saimaa ringed seal (Pusa saimensis), an endangered freshwater pinniped endemic to Lake Saimaa, Finland. The assembly spans 2.353 Gb and comprises 15 autosomes together with the X and Y sex chromosomes. Using Oxford Nanopore Technologies (ONT) long-read sequencing and Hi-C scaffolding, we achieved a telomere-to-telomere assembly for all chromosomes, except the Y chromosome. Genome annotation identified approximately 21,800 protein-coding genes, consistent with other mammalian genomes. Assembly completeness was high, with BUSCO analysis recovering 99.6% of expected complete single-copy genes (98.2% single-copy and 1.3% duplicated). Comparative analyses revealed a highly conserved chromosomal architecture, with only minor syntenic differences relative to other pinniped chromosome-level assemblies. Previously described cytogenetic fusion events in Phocidae were confirmed (chromosomes 2 and 7). A translocation between chromosomes 6 and 7 distinguishes phocids from the otariids. In general, more distantly related taxa exhibit an increasing degree of intrachromosomal rearrangements. Notably, we identified a large intrachromosomal rearrangement on chromosome 2 that appears specific to the Saimaa ringed seal. Phylogenomic analysis based on 9,226 single-copy orthologues placed the Saimaa ringed seal as a sister lineage to the Baltic ringed seal (Pusa hispida botnica), while confirming also other established evolutionary relationships among pinnipeds. Comparative gene family analysis between the Saimaa ringed seal and the closely related grey seal (Halichoerus grypus) revealed lineage-specific differences driven by a limited number of gene families. In the Saimaa ringed seal, expansions were observed in ion transport, cytoskeleton, and regulatory genes, potentially reflecting adaptation to freshwater conditions. In contrast, the grey seal showed expansions in olfaction, immune-and spermatogenesis-associated gene families, including MAGE/MIA genes, consistent with differences in ecology and mating systems. This reference genome provides an important resource for studies of pinniped genome evolution, as well as conservation and population genomics of the Saimaa ringed seal, facilitating future work on genetic diversity, inbreeding, mutational load and adaptive potential in this highly endangered species.

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

Preclinical Efficacy of Tasquinimod in Myelodysplastic Neoplasms: Restoring Erythropoiesis and Mitigating Bone Loss

Myelodysplastic neoplasms (MDS) are clonal disorders characterized by ineffective hematopoiesis, dysplasia, and a risk of transformation into acute myeloid leukemia. MDS is also associated with a higher incidence of osteoporosis, suggesting a complex interplay between hematopoiesis, the bone marrow (BM) microenvironment, and bone homeostasis. Targeting inflammation has emerged as a promising therapeutic strategy, particularly in lower-risk MDS. Tasquinimod (TASQ) is a small-molecule inhibitor of the inflammatory alarmin S100A9, blocking its interaction with TLR4 and RAGE receptors. We investigated the efficacy of TASQ in modulating inflammation and improving disease phenotype using in vitro and in vivo MDS models. Immunofluorescence staining of human BM identified neutrophils and macrophages as primary S100A9 sources. Exposure of mesenchymal stromal cells (MSCs) to S100A9 induced TLR4 downstream signaling, resulting in increased expression of IRAK1, NF-{kappa}B-p65, IL-1{beta}, IL-18, caspase 1 and PD-L1. These effects were effectively abolished by TASQ. Additionally, TASQ restored the disturbed MSC-mediated hematopoietic support, as demonstrated by increased numbers of cobblestone area-forming cells and colony-forming units. In NHD13 MDS mice, TASQ (30 mg/kg, 12 weeks) improved hemoglobin and red blood cell counts, but exerted no effect in wild-type (WT) mice. Additionally, TASQ improved bone microarchitecture by increasing trabecular number and bone volume, likely a result of reduced osteoclast activity. Our findings suggest that TASQ mitigates inflammasome activation in the MDS BM, improving erythropoiesis and bone health. These results provide a necessary preclinical basis for clinical trials in lower-risk MDS patients, in whom anemia and osteoporosis often coexist.

cell biology↗

bioRxiv2025

Identification of immune response genes of cassava during early phases of cassava brown streak virus infection

Cassava brown streak disease (CBSD) caused by the ipomoviruses CBSV and UCBSV, poses a significant threat to cassava crops and the destruction of tuberous roots leads to substantial yield losses. Virus resistance identified in some South American cassava germplasm lines inhibits virus replication and movement and, is a complete immunity of some lines or, a restriction of the virus replication to phloem companion cells and root infection in others. To further explore the resistance responses and identify potential resistance genes, a time-course RNA-Seq study was conducted comparing gene expression of a virus-susceptible cassava TMS 96/0304 with a cassava line restricting CBSV to the roots and a cassava DSC 167 (COL2182), immune to the virus. Differential gene expression patterns across leaves, stems, and roots revealed substantial differences between susceptible and resistant genotypes. Temporal analysis highlighted significant variations in the number of differentially expressed genes (DEGs), particularly in stem tissues at one day after inoculation (DAI), with notable overexpression observed in the resistant lines DSC 167 (436 DEGs) and DSC 260 (335 DEGs). In contrast, significant expression changes were noted only at 10 DAI in the virus infected TMS 96/0304 (737 DEGs). Several DEGs in resistant genotypes were associated with proteins involved in hormonal regulation, defense and immunity, transcriptional regulation, stress response, cell structure, and signal transduction. The analysis indicates that virus resistance in the studied lines is driven by early-stage regulation of genes for which specific functions remain to be elucidated.

plant biology↗

bioRxiv2025

Near-chromosome-level genome assembly and transcriptome of the Ural owl, Strix uralensis PALLAS, 1771

The Ural owl (Strix uralensis) is a large member of the Strigidae family and inhabits Eurasian forests ranging from Germany to Japan. However, it faces increased range reduction, particularly at its southwestern distribution edges. Despite being considered "Least Concern" by the IUCN, local populations have become threatened in Central Europe due to severe habitat loss. Reintroduction programs aim to restore these populations by closing distribution gaps and facilitating natural recolonization of suitable habitats. To support these efforts, genomic resources have become an established tool to assess genetic diversity, geographic structure, and potential inbreeding, crucial for maintaining the genetic health and adaptability of newly established populations. Here, we present a de novo genome assembly and transcriptome of the Ural owl based on ONT long-reads, Omni-C Illumina short-reads, and RNASeq data. The final assembly has a total length of 1.26 Gb, of which 96.37 % are anchored into the 41 largest scaffolds. The contig and scaffold N50 values of 88.6 Mb and 21.7 Mb, respectively, a BUSCO/compleasm completeness of 97.5 %/99.65 % and k-mer completeness of 95.18 %, emphasize the high quality of this assembly. Furthermore, annotation of the assembly identified 17,650 genes and a repeat content of 12.48 %. This new highly contiguous and chromosome-scale assembly will greatly benefit Ural owl conservation management by informing reintroduction programs about the species genetic health and contributing a valuable resource to study genetic function in greater detail across the whole Strigidae family.

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

Heparin flexibility within the extracellular matrix determines the bioactivity of bound vascular endothelial growth factor

Vascular endothelial growth factor (VEGF), a major regulator of blood vessel formation, is naturally bound to heparan sulfate proteoglycans in the extracellular matrix (ECM). Yet, how the physical presentation of VEGF by the matrix impacts its signaling potential remains fully unknown. To address this question, we have developed a tunable heparin-containing hydrogel model that recapitulates natural VEGF binding modes with full and independent control over physical properties. Using this model, we show that the degree of heparin flexibility in the hydrogel network determines the mobility of bound VEGF and, in turn, its ability to interact with VEGF receptor 2. We demonstrate that VEGF mobility is driven by a relay mechanism, in which VEGF molecules directly switch from one heparin chain to another. When strong electrostatic interactions between heparin and other hydrogel constituents immobilize the sugar backbone, this relay mechanism is impeded, in turn reducing VEGFs ability to reach its target receptor at the cell membrane, thereby reducing its bioactivity. This work identifies heparin flexibility within the ECM as a previously unknown regulator of the microenvironment, which will not only contribute to a better mechanistic understanding of how the ECM regulates growth factor bioactivity, but it will also provide an important design criterion for the development of tissue-engineered biomaterials that require vascularization.

bioengineering↗

bioRxiv2025

Rhizoctonia theobromae associated with a severe witches' broom outbreak in cassava of the Brazilian rainforest and evidence of its Southeast Asian origin

Cassava witches broom disease (CWBD) has emerged as a significant threat to cassava production in the Oiapoque region of Amapa, Brazil. Diseased plants exhibit stunted growth, vascular necrosis, abnormal shoot proliferation, and distinctive broom-like appearance. This study aimed to characterize the disease and identify its causal agent(s). The assessment by high-throughput sequencing of total nucleic acids (DNA and RNA) from affected cassava tissues revealed Rhizoctonia theobromae (syn. Ceratobasidium theobromae) associated with CWBD. PCR-based detection using species-specific primers confirmed the presence of R. theobromae in 74% of symptomatic samples. Genetic diversity analysis based on the Ca2+/calmodulin-dependent protein kinase gene showed low variability among Brazilian isolates compared with Asian populations, suggesting their recent introduction. This first report of R. theobromae causing CWBD in Brazil follows a recent report of the disease from French Guiana and highlights the urgent need for effective measures to prevent the further spread of this emerging pathogen, which poses a deadly threat to cassava cultivation in the rainforest, a significant risk to cassava production in Brazil, and regions with similar eco-climatic conditions.

pathology↗

bioRxiv2024

Inflammatory Mesenchymal Stromal Cells and IFN-responsive T cells are key mediators of human bone marrow niche remodeling in CHIP and MDS

Somatic mutations in hematopoietic stem/progenitor cells (HSPCs) can lead to clonal hematopoiesis of indeterminate potential (CHIP), potentially progressing to myelodysplastic syndromes (MDS). Here, we investigated how CHIP and MDS remodel the human bone marrow (BM) niche relative to healthy elderly donors, using single cell and anatomical analyses in a large BM cohort. We found distinct inflammatory remodeling of the BM in CHIP and MDS. Furthermore, the stromal compartment progressively lost its HSPC-supportive adipogenic CXCL12-abundant reticular cells while an inflammatory mesenchymal stroma cell (iMSCs) population emerged in CHIP, which expanded in MDS. iMSCs exhibited distinct functional signatures in CHIP and MDS, retaining residual HSPC-support and angiogenic activity in MDS, corresponding with an increase in microvasculature in the MDS niche. Additionally, an IFN-responsive T cell population was linked to fueling inflammation in the stroma. Overall, these findings open new avenues for early intervention in hematological malignancies.

molecular biology↗

bioRxiv2024

The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12

Cassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary source of food and income. However, cassava production is threatened by several viral diseases, including cassava brown streak disease, which causes severe damage to the edible storage roots. Current cassava varieties in Africa lack effective resistance to this disease, leading to significant crop losses. We investigated the genetic diversity of cassava and identifed new sources of resistance to the viruses causing cassava brown streak disease. The cassava line, COL40, from a South American germplasm collection showed broad-spectrum resistance against all known strains of the viruses that cause this disease. To further understand the genetic basis of this resistance, we sequenced the genome of COL40 and produced a high-quality, haplotype-resolved genome assembly. This genomic resource provides new insights into cassavas genetic architecture, particularly in regions associated with disease resistance. The sequence reveals significant structural variation, including transposable elements, inversions, and deletions, which may contribute to the resistance phenotype. The reference genome assembly presented here will provide a valuable genomic resource for studying the cassava brown streak resistance and will help in accelerating breeding efforts to introduce virus resistance into African cassava varieties. By identifying genetic variants linked to resistance, future breeding programs can develop cassava cultivars that are more resilient to viral threats, enhancing food security and livelihoods for smallholder farmers across regions affected by the disease.

genomics↗

bioRxiv2024

Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods

Modern DNA-based biodiversity surveys result in massive-scale data, including up to millions of species - of which most are rare. Making the most of such data for inference and prediction requires modelling approaches that can relate species occurrences to environmental and spatial predictors, while incorporating information about their taxonomic or phylogenetic placement. Even if the scalability of joint species distribution models to large communities has greatly advanced, incorporating hundreds of thousands of species has not been feasible to date, leading to compromised analyses. Here we present a novel "common to rare transfer learning" approach (CORAL), based on borrowing information from the common species to enable statistically and computationally efficient modelling of both common and rare species. We illustrate that CORAL leads to much improved prediction and inference in the context of DNA metabarcoding data from Madagascar, comprising 255,188 arthropod species detected in 2874 samples.

ecology↗

bioRxiv2024

Unraveling Genome- and Immunome-wide Genetic Diversity in Jaguars (Panthera onca): Implications for Targeted Conservation

Our study examines the declining Jaguar populations in Central and South America, assessing the impact of habitat loss and fragmentation on genetic diversity and local adaptation. We investigated population structure and immunome variability in 25 jaguars to identify unique genetic diversity for informed, targeted conservation. Our genome-wide analyses revealed three distinct geographic populations corresponding to Central America, South American lowland, and South American highland regions. While the highland population displayed lower overall immunome-wide variability, specific innate (Natural killer cell complex, Toll-like receptor) and adaptive (Major histocompatibility complex-class-II) immune genes crucial for adaptive responses showed promising diversity. Nonetheless, South American highland and Central American jaguars are severely threatened. Therefore, we propose re-evaluating evolutionary significant units to prioritize conservation efforts, preserving crucial genetic and adaptive diversity essential for the species resilience and long-term survival.

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↗

bioRxiv2023

Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university masters course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 - 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.

genomics↗

bioRxiv2023

APOE, Immune Factors, Sex, and Diet Interact to Shape Brain Networks in Mouse Models of Aging

Alzheimers disease (AD) presents complex challenges due to its multifactorial nature, poorly understood etiology, and late detection. The mechanisms through which genetic, fixed and modifiable risk factors influence susceptibility to AD are under intense investigation, yet the impact of unique risk factors on brain networks is difficult to disentangle, and their interactions remain unclear. To model multiple risk factors including APOE genotype, age, sex, diet, and immunity we leveraged mice expressing the human APOE and NOS2 genes, conferring a reduced immune response compared to mouse Nos2. Employing graph analyses of brain connectomes derived from accelerated diffusion-weighted MRI, we assessed the global and local impact of risk factors in the absence of AD pathology. Aging and a high-fat diet impacted extensive networks comprising AD-vulnerable regions, including the temporal association cortex, amygdala, and the periaqueductal gray, involved in stress responses. Sex impacted networks including sexually dimorphic regions (thalamus, insula, hypothalamus) and key memory-processing areas (fimbria, septum). APOE genotypes modulated connectivity in memory, sensory, and motor regions, while diet and immunity both impacted the insula and hypothalamus. Notably, these risk factors converged on a circuit comprising 63 of 54,946 total connections (0.11% of the connectome), highlighting shared vulnerability amongst multiple AD risk factors in regions essential for sensory integration, emotional regulation, decision making, motor coordination, memory, homeostasis, and interoception. These network-based biomarkers hold translational value for distinguishing high-risk versus low-risk participants at preclinical AD stages, suggest circuits as potential therapeutic targets, and advance our understanding of network fingerprints associated with AD risk. Significance StatementCurrent interventions for Alzheimers disease (AD) do not provide a cure, and are delivered years after neuropathological onset. Addressing the impact of risk factors on brain networks holds promises for early detection, prevention, and revealing putative therapeutic targets at preclinical stages. We utilized six mouse models to investigate the impact of factors, including APOE genotype, age, sex, immunity, and diet, on brain networks. Large structural connectomes were derived from high resolution compressed sensing diffusion MRI. A highly parallelized graph classification identified subnetworks associated with unique risk factors, revealing their network fingerprints, and a common network composed of 63 connections with shared vulnerability to all risk factors. APOE genotype specific immune signatures support the design of interventions tailored to risk profiles.

neuroscience↗

bioRxiv2023

Genomic analysis reveals limited hybridization among three giraffe species in Kenya

BackgroundIn the speciation continuum the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. ResultsWe found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. ConclusionsDespite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.

evolutionary biology↗

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↗