Mining livestock genome datasets for an unconventional characterization of animal DNA viromes

Bovo, Samuele; Schiavo, Giuseppina; Bolner, Matteo; Ballan, Mohamad

doi:10.1016/j.ygeno.2022.110312

Cited by 8 publications

(6 citation statements)

References 95 publications

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“…Datasets from wild boars were also retrieved from the same database: two were from wild boars of the Near East region; 18 from wild boars of Asia; and 14 from wild boars of Europe. More details of this dataset and related sequencing-derived statistics are reported in Bovo et al [ 16 ] and in Table S1 ; ENA datasets (publicly available) were obtained from a DNA pooling strategy (DP > 20X). This dataset consisted of 22 DNA pools (constructed from 30–35 pigs each), representing 22 different European breeds and one European wild boar population.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Animals 2024, 14, 5 16 of 19 reported to be in high LD with the 2.3 kb deletion (allele O) that probably occurred between 3.5 and 10 MYBP. The allele distribution of these two polymorphic sites, together with several other SNVs and SVs, have been investigated in several tens of pig breeds, providing a general picture of variability in the ABO gene in many pig populations of different origins.…”

Section: Supplementary Materialsmentioning

confidence: 99%

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Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Bolner,

Bertolini,

Bovo

et al. 2023

Animals

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Polymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Supplementary Materialsmentioning

confidence: 99%

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Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Bolner,

Bertolini,

Bovo

et al. 2023

Animals

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“…Recent functional annotation of three domestic animal genomes (cattle, chicken, and pig) provides a useful resource for livestock research (57). The study of the genome is pertinent to many areas of research, including ancestry determination, genomic selection, and vaccine and drug design (58)(59)(60).…”

Section: Assembly and Annotation Of Newly Sequenced Genomesmentioning

confidence: 99%

Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science

Pathak

Kim

2022

Front. Vet. Sci.

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Having played important roles in human growth and development, livestock animals are regarded as integral parts of society. However, industrialization has depleted natural resources and exacerbated climate change worldwide, spurring the emergence of various diseases that reduce livestock productivity. Meanwhile, a growing human population demands sufficient food to meet their needs, necessitating innovations in veterinary sciences that increase productivity both quantitatively and qualitatively. We have been able to address various challenges facing veterinary and farm systems with new scientific and technological advances, which might open new opportunities for research. Recent breakthroughs in multi-omics platforms have produced a wealth of genetic and genomic data for livestock that must be converted into knowledge for breeding, disease prevention and management, productivity, and sustainability. Vetinformatics is regarded as a new bioinformatics research concept or approach that is revolutionizing the field of veterinary science. It employs an interdisciplinary approach to understand the complex molecular mechanisms of animal systems in order to expedite veterinary research, ensuring food and nutritional security. This review article highlights the background, recent advances, challenges, opportunities, and application of vetinformatics for quality veterinary services.

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“…However, these prior studies have mainly investigated diseased animals, while the normal viral community of healthy birds and how it varies among populations and over time remain unexplored. Currently, next-generation sequencing (NGS) is extensively used in virus discovery in humans and livestock, enabling unbiased detection of enormous viral sequence datasets [9,10]. The aim of our study was to use NGS to determine the differential virus community of healthy broiler flocks and broiler flocks affected by RSS.…”

Section: Introductionmentioning

confidence: 99%

Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks

Kubacki

Qi²,

Fraefel

2022

Microorganisms

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The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases.

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Mining livestock genome datasets for an unconventional characterization of animal DNA viromes

Cited by 8 publications

References 95 publications

Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science

Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks

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