Biology subjects

Crepaldi, P.

Publications and source records attributed to Crepaldi, P..

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↗

bioRxiv2025

Inferring domestic goat demographic history through ancient genome imputation

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this we used published high coverage (>8x) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5x genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with [≥]0.5x coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes. SignificancePaleogenomics offers crucial insight into how animals were domesticated, but poor DNA preservation in ancient remains often limits the reach of genetic analyses. We utilise a cutting-edge technique, genotype imputation, to recover missing genetic information from ancient low coverage goat genomes and shine light on their domestication process. Early domestic goats showed low overall runs-of-homozygosity (ROH) and relatedness. We find that during the Neolithic, runs-of-homozygosity (ROH) and relatedness among goats increased, likely a consequence of the movement of herds beyond their natural range by humans. Inbreeding levels decline in more recent periods, potentially due to expanded herd sizes, animal trade networks, or improved husbandry practices. These findings challenge long-standing assumptions about domestication bottlenecks and highlight how ancient DNA can be used to uncover complex evolutionary histories, even from low coverage ancient samples.

genomics↗