Ruvinskiy, D. | bioRxiv Science

bioRxiv2025

Unmapped reads from whole-genome sequencing data reveal pathogen diversity in European and African cattle breeds

Climate change is impacting the global spread of infectious diseases, altering pathogen distribution and transmission, threatening human and animal health. This study investigates the presence of potential pathogens in blood within unmapped reads obtained from whole-genome sequencing data of various cattle breeds across geographically diverse regions, including South Africa, Uganda, Egypt, Portugal, The Netherlands, and Finland. Unmapped reads were extracted, assembled into contigs, and subjected to taxonomic analysis based on an extensive literature search. The analysis revealed significant geographic variation in pathogen composition, with breeds in the Southern Hemisphere (Uganda, Egypt, and South Africa) showing higher alignment pathogen counts while northern breeds (particularly from Finland) exhibited lower diversity and counts. Portugal, representing a transition zone, exhibited a higher burden of parasites and tick-borne related pathogens which were also prevalent in Southern Hemisphere breeds such as Theileria parva, Anaplasma platys, Theileria orientalis, and Babesia bigemina, which is in line with the known capacity of these breeds to cope with local pathogens. Dutch breeds were found to harbor Escherichia coli O157, a known public health concern. The study provided key insights into emerging disease risks influenced by climate change and livestock management practices. This study highlights the potential for climate-driven variations in disease ecology and transmission, emphasizing the need for integrating genomic and environmental data and is currently the most comprehensive study to date investigating the microbial diversity present in unmapped reads obtained from WGS data of cattle populations. HighlightsO_LIUnmapped sequence reads analysis of blood reveals signatures of disease occurrence over time. C_LIO_LIBlood pathogens prevail in the Southern hemisphere, becoming less evident towards northern regions (i.e. we observed a gradient pattern), with Portugal (and partly the Netherlands) showing intermediate values. C_LIO_LIThe commercial Holstein cattle in the six countries exhibited lower pathogen sequence alignments than their native counterparts (i.e. the Netherlands). C_LI

bioinformatics↗

bioRxiv2023

Adipose gene expression profiles and their associations with adaptations in Northern Finncattle, Mirandesa cattle, Yakutian cattle and Holstein cattle

BackgroundThe drastic change in global climate has led to in-depth studies of the genetic resources of native cattle adapted to challenging environments. Native cattle breed data may harbor unique variants that will enable the generation of new tools to improve the adaptation potential of commercial cattle breeds. Adipose tissues are key factors in the regulation of metabolism and energy balance and are crucial for the molecular switches needed to adapt to rapid environmental and nutritional changes. The transcriptome landscape of four adipose tissues was used in this study to investigate the effect of the environment on the gene expression profiles of three local breeds, Yakutian cattle (Sakha Republic), Northern Finncattle (Finland), Mirandesa cattle (Portugal) and commercial Holstein cattle. ResultsA total of 26 animals (12 cows, 14 bulls) yielded 81 samples of perirenal adipose tissue (n=26), metacarpal adipose tissue (n=26), tailhead adipose tissue (n=26) and prescapular adipose tissue (n=3). More than 17,000 genes were expressed in our dataset. Principal component analysis of the normalized expression profiles revealed a differential expression profile of the metacarpal adipose tissue. We found that the genes upregulated in the metacarpal adipose tissue of Yakutian cattle, such as NR4A3, TEKT3, and FGGY, were associated with energy metabolism and response to cold temperatures. In Mirandesa cattle, the upregulated genes in perirenal adipose tissue were related to immune response and inflammation (AVPR2, CCN1, and IL6), while in Northern Finncattle, the upregulated genes appeared to be involved in various physiological processes, including energy metabolism (IGFBP2). According to the sex-based comparisons, the most interesting result was the upregulation of the TPRG1 gene in three tissues of Yakutian cattle females, suggesting that adaptation is related to feed efficiency. ConclusionsThe highest number of differentially expressed genes was found between Yakutian cattle and Holstein, several of which were associated with immunity in Yakutian cattle, indicating potential differences in disease resistance and immunity between the two breeds. This study highlights the vast difference in gene expression profiles in adipose tissues between breeds from different climatic environments, most likely highlighting selective pressure and the potential significance of the uniquely important regulatory functions of metacarpal adipose tissue.

genomics↗