Biology subjects

Bionda, A.

Publications and source records attributed to Bionda, A..

4 recordsLinked to original sources

bioRxiv2026

Linking geography and mutation profiles across goat species

Recent studies have characterised the mutational profile across multiple mammalian species, highlighting substantial differences across lineages. However, none of these studies investigated whether mutation profiles and geography are significantly correlated. In this study, we present a multi-genome alignment spanning several Capra taxa, reconstruct the ancestral genome of Capra hircus and use it to characterize the mutational profiles across multiple Capra species by using the 1000 genomes VarGoats dataset. Results confirmed that the scale of differences among Capra species largely reflects their phylogenetic relationships, in particular with the Bezoar being genetically closer to domestic goats than to other wild species. Subsequently, we correlated the mutational profile and the geographical origin of the different individuals. In particular, ACG>ATG changes have the strongest correlation with longitude (r = -0.79, P-value = 3.02*10-204), while TCA>TGA are strongly correlated with latitude (r = -0.51, P-value = 4.30*10-63). We highlight how sequential dinucleotide mutations (SDMs) place cosmopolitan breeds closer to the sampling location, rather than the country of origin, showing how the recent relocation of cosmopolitan breeds to new continents is reshaping the genome of these animals. Finally, we used the mutational profile to predict the coordinate of origin of each animal in the dataset. In conclusion, we show the important role that geography had in shaping the genomes of domestic goats.

genomics↗

bioRxiv2025

A tailored variant filtering procedure for multi-breed and multi-species unbalanced animal SNP collections

Technological advancements and decreasing costs of whole-genome sequencing have generated a huge amount of resequencing data. Large-sized datasets, spanning several species and/or populations can now be assembled easily. However, they vary widely in geographical provenance, and sample sizes, with taxonomic groups varying from single to hundreds of entries. Consequently, standard filtering approaches may bias the representation of groups or gene pools. Commonly adopted variant filters relying on minor allele frequency (MAF) and linkage disequilibrium (LD) are not adequate because LD patterns and allele frequencies differ substantially within datasets representing both local and global diversity of multiple populations and species. Thus, by using the VarGoats 1000 goat genome project, we devised a novel approach which avoids the biases of the standard filtering procedures by adopting within-population subsampling, minor allele count (MAC) and marker spacing (bp-space) as filters. Starting from a quality-filtered dataset of >28M SNPs from 1372 animals, we generated a dataset of <14M markers and 750 individuals, complying with the initial requirements and facilitating further computational steps.

bioinformatics↗

bioRxiv2025

The variability of goat microRNA genes is strongly shaped by functional constraints

BackgroundMicroRNAs (miRNAs) are a type of small non-coding RNAs involved in the post-transcriptional repression of target mRNA transcripts, and responsible for the fine-tuning of numerous molecular mechanisms regulating cell metabolism. In goats, multiple miRNAs are involved in coordinating the expression of networks of genes with key roles on the phenotypic variation of milk and meat traits. Although a comprehensive set of goat miRNAs has been annotated, their levels of polymorphism have not been characterized yet. Such information would be relevant in order to explore the effects of miRNA variants on phenotypes of economic interest in goats. ResultsBy using whole-genome sequencing data from 770 domestic goats with African, Asian, and European origins, we have identified polymorphic sites located within miRNA genes as well as in their flanking regions. In doing so, we have found that miRNA polymorphisms are rare (median alternative allele frequency of 0.46%) and that the distribution of polymorphic sites within and around miRNA loci is uneven. Remarkably, the stem, loop and neighbouring regulatory regions of precursor miRNA hairpins show a significantly higher polymorphism density compared to the miRNA seed, which determines the binding affinity to target mRNAs. Moreover, we have detected a differential segregation of miRNA variants across and within continental regions, with an enriched segregation of putatively high impact polymorphisms, i.e. those located in the seed and other biologically relevant regions of miRNA genes, in isolated goat populations with a low census and elevated content of runs of homozygosity. ConclusionGoat miRNA genes display low levels of variation particularly in the seed region, likely due to the action of strong purifying selection removing mutations with potential effects on gene regulatory networks linked to miRNA function. Moreover, miRNA polymorphisms tend to be more abundant in goat breeds with high levels of homozygosity, likely because purifying selection is less efficient in populations of limited size. The information provided in the current work could be useful to identify miRNA polymorphisms contributing to phenotypic variation through the disruption of gene regulatory networks in domestic goats, as well as to assess their potential impact on adaptation and fitness.

genomics↗

bioRxiv2021

Echocardiographic mitral valve association with morphometric measurements in Cavalier King Charles Spaniels via Inverse Probability Weighting analysis

Development and progression of myxomatous mitral valve disease (MMVD) in Cavalier King Charles Spaniels (CKCS) are difficult to predict. Identification at a young age of dogs with a morphotype associated with more severe mitral disease is desirable. The aims of this study were to: 1) describe the physical, morphometric, and echocardiographic features of MMVD affected Cavalier King Charles Spaniels (CKCS) in American College of Veterinary Internal Medicine (ACVIM) class B1; 2) evaluate the influence of morphometric physical measurements on murmur intensity, mitral valve prolapse (MVP), regurgitant jet size and indexed mitral valve and annulus measurements. Fifty-two MMVD affected CKCS in ACVIM class B1 were included. This is a prospective clinical cross-sectional study. Morphometric measurements, which included body, thorax, and the head sizing of each dog, have been investigated to establish the association with heart murmur intensity, valvular and annular echocardiographic measurements, MVP and regurgitant jet size using inverse probability weighting (IPW) analyses to adjust for confounding. The IPW analyses showed that when head length and nose length decreased, dogs had more severe regurgitant jet size. Furthermore, subjects with more pronounced head stop angle had thicker anterior mitral valve leaflets. A brachycephalic morphotype, with dogs more similar to King Charles Spaniel breed in cephalic morphology, is associated with a more severe regurgitant jet size and with valvular characteristics related to worse forms of MMVD.

pathology↗