Biology subjects

Farre, M.

Publications and source records attributed to Farre, M..

5 recordsLinked to original sources

bioRxiv2025

Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus

Sorex araneus, the Eurasian common shrew, has seasonal brain size plasticity (Dehnels phenomenon) and abundant intraspecific chromosomal rearrangements, but genomic contributions to these traits remain unknown. We couple a chromosome-scale genome assembly with seasonal brain transcriptomes to discover relationships between molecular changes and both traits. Positively selected genes enriched the Fanconi anemia DNA repair pathway, which prevents the accumulation of chromosomal aberrations, and is likely involved in chromosomal rearrangements (FANCI, FAAP100). Genes involved in neurogenesis show either signatures of positive selection (PCDHA6), seasonal differential expression in the cortex and hippocampus (Notch signaling), or both (SOX9), suggesting a role for cellular proliferation in seasonal brain shrinkage and regrowth. Both positive selection and evolutionary upregulation in the shrew hypothalamus of VEGFA and SPHK2 indicate adaptations in hypothalamic metabolic homeostasis have evolved together with Dehnels phenomenon. These findings reveal genomic changes central to the evolution of both chromosomal instability and cyclical patterns in brain gene expression that characterizes mammalian brain size plasticity. TeaserGenomic and expression variations are key to chromosomal instability and seasonal brain plasticity in the common shrew.

evolutionary biology↗

bioRxiv2025

Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck

Advances in the sequencing and assembly of chromosome-level genome assemblies has enabled the study of non-model animals, providing further insights into the evolution of genomes and chromosomes. Here, we present the waterbuck (Kobus ellipsiprymnus) as an emerging model antelope for studying population dynamics and chromosome evolution. Antelope evolutionary history has been shaped by Robertsonian (Rb) fusions, with waterbuck also showing variation in karyotype due to two polymorphic Rb fusions. These polymorphisms are variable between and within the two recognised subspecies, the common and defassa waterbuck. To provide new insights into waterbuck evolution, we firstly assembled a chromosome-level genome assembly for the defassa subspecies using PacBio HiFi and Hi-C sequencing. We then utilised museum collections to carry out whole genome sequencing (WGS) of 24 historical waterbuck skins from both subspecies. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date. We found novel population structure and gene flow between waterbuck populations and regions across the genome with high genomic differentiation between the two subspecies. Several of these regions were found around the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. Interestingly, these regions contain genes involved in development, fertility, and recombination. Our results highlight the importance of assembling genomes to the chromosome-level, the utility and value of historical collections in sampling a wide-ranging species to uncover fine-scale population structure, and the potential impacts of Rb fusions on genomic differentiation and the recombination landscape.

evolutionary biology↗

bioRxiv2024

Global Prevalence of Cryptosporidium Infections in Cattle and C. parvum genotype distribution: A Meta-Analysis

BackgroundThe protozoan parasite Cryptosporidium is the causative agent of a severe diarrhoeal disease, called cryptosporidiosis. Cryptosporidium species are capable of infecting a wide range of hosts including humans and livestock. In cattle, cryptosporidiosis is now one of the most important causes of neonatal scour globally, either as a sole agent or co-infecting with other pathogens. Cryptosporidiosis is considered globally endemic, with a prevalence of Cryptosporidium in stool samples from 13% to 93% in European cattle. This disease has a significant economic burden, with costs associated with veterinary diagnosis, medication, increased labour, animal rearing and supplemental nutrition as well as being associated with reduced long-term growth rate in calves, causing huge economic losses in livestock industry. Moreover, cattle act as a zoonotic reservoir for Cryptosporidium parvum, a species that is capable of infecting humans as well. As such, monitoring the prevalence of Cryptosporidium in cattle is important due to the public health risk and financial burden the clinical disease causes. MethodsPublications reporting on the prevalence of Cryptosporidium in cattle were collected from PubMed and Google Scholar. Information regarding the species of Cryptosporidium in positive samples, the genotype of C. parvum found in samples, and the diarrhoeic status of the cattle was collected where available. A total of 279 publications were collected for this meta-analysis from six continents and 65 countries to provide an estimation for global bovine Cryptosporidium prevalence. ResultsA 25.5% global prevalence of Cryptosporidium infection was reported, with C. parvum being the most frequently identified species, particularly the IIa subfamily. Diarrhoea was reported in 14,141 cattle samples, of which 36.0% tested positive for Cryptosporidium. Regarding symptoms, we found that in countries reporting over 50% of diarrhoeic positive cattle, C. parvum was the most common species. ConclusionsContinued monitoring and reporting of Cryptosporidium in cattle are crucial for both public health and economic reasons. Consequently, efforts should focus on underreported regions and the development of control measures to reduce prevalence and limit zoonotic transmission.

microbiology↗

bioRxiv2024

Structure, substrate selectivity determinants and membrane interactions of a Glutamate-specific TAXI TRAP binding protein rom Vibrio cholerae.

Tripartite ATP independent periplasmic (TRAP) transporters are widespread in prokaryotes and are responsible for the transport of a variety of different ligands, primarily organic acids. TRAP transporters are secondary active transporters that employ a substrate binding protein to bind and present the substrate to membrane embedded translocation component. TRAP transporters can be divided into two subclasses; DctP-type and TAXI type, which share the same overall architecture and requirement of the SBP for transport, but their SBPs share no similarity. The DctP-type transporters are very well studied and have been shown to transport a range of compounds including dicarboxylates, keto acids, sugar acids. However, the TAXI type transporters are relatively poorly understood, with the range of transportable compounds still to be discovered and selectivity requirements for binding unknown. To address these shortfalls in our understanding, we have structurally and biochemically characterized VC0430 from Vibrio cholerae revealing it to be a monomeric high affinity glutamate binding protein. VC0430 is stereoselective, binding the L-isomer preferentially, and can also bind L-glutamine and L-pyroglutamate, but with low affinity relative to L-glutamate. Structural characterization of ligand bound VC0430 reveals details of the binding site and biophysical characterization of binding site mutant reveal the substrate binding determinants, which differ substantially from the DctP-type TRAPs. Finally, we have analysed in silico the interaction between VC0430 and its cognate membrane component revealing an architecture hitherto unseen. To our knowledge, this is the first transporter in V. cholerae to be identified as specific to glutamate, which plays a key role in osmoadaptation of V. cholerae, making this transporter a potential therapeutic target.

biochemistry↗

bioRxiv2019

Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

Once recombination is halted between the X and Y chromosome, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about variation in sex chromosome differentiation within clades. Here, we combined whole genome and transcriptome sequencing data to characterise the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged 30 mya. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata are largely homomorphic, with recombination persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely non-recombining and strikingly heteromorphic. ln addition to being highly divergent, the sex chromosome system in P. picta includes a neo-sex chromosome, the result of a fusion between the ancestral sex chromosome and part of chromosome 7. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of complete dosage compensation in this species, the first such documented case in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

evolutionary biology↗