Armand Sanchez

Autonomous University of Barcelona | UAB · Department of Animal and Food Science

The intramuscular oleic‐to‐stearic fatty acid ratio (C18:1n‐9/C18:0) is an important indicator of the biosynthesis and desaturation of fatty acids in muscle. By using an RNA‐Seq approach in muscle samples from 32 BC1_DU (25% Iberian and 75% Duroc) pigs with divergent values (high: H and low: L) of C18:1n‐9/C18:0 fatty acids ratio, a total of 81 dif...

Background The composition and distribution of fatty acids (FA) are important factors determining the quality, flavor, and nutrient value of meat. In addition, FAs synthesized in the body participate in energy metabolism and are involved in different regulatory pathways in the form of signaling molecules or by acting as agonist or antagonist ligand...

Background Goats were domesticated in the Fertile Crescent about 10,000 years before present (YBP) and subsequently spread across Eurasia and Africa. This dispersal is expected to generate a gradient of declining genetic diversity with increasing distance from the areas of early livestock management. Previous studies have reported the existence of...

In pigs, meat quality depends markedly on the fatty acid (FA) content and composition of the intramuscular fat, which is partly determined by the gene expression in this tissue. The aim of this work was to identify the link between muscle gene expression and its FA composition. In an (Iberian × Duroc) × Duroc backcrossed pig population, we identifi...

Non-invasive genetic analysis allows for monitoring and understanding population dynamics without disturbing wild animals. We present a non-invasive genetic method to identify and characterize the Cantabrian and Pyrenean (of Slovenian origin) brown bear populations. We selected an efficient panel of 61 SNPs to genotype more than 2,000 non-invasive...

Background Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and putative regulators involved in FA composition, we performed a multivariate integrative analysis between intramuscular FA and transcriptome profiles...

The gut microbiota is a key player in the host metabolism. Some bacteria are able to ferment non-digestible compounds and produce short-chain fatty acids that the host can later transform and accumulate in tissue. In this study, we aimed to better understand the relationships between the microorganisms and the short-chain fatty acid composition of...

Polyunsaturated fatty acids (PUFA), such as omega-6 (n-6) and omega-3 (n-3), play a vital role in nutrient metabolism, inflammatory response and gene regulation. microRNAs (miRNA), which can potentially degrade targeted messenger RNAs (mRNA) and/or inhibit their translation, might play a relevant role in PUFA-related changes in gene expression. Alt...

The mammalian spermatozoon has a unique chromatin structure in which the majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The sperm’s chromatin structure remains unresolved in most animal species, including the pig. However, mapping the genom...

Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids with antagonistic inflammatory functions that play vital roles in metabolic health and immune response. Current commercial swine diets tend to over-supplement with n-6 PUFAs, which may increase the likelihood of developing inflammatory diseases and affect...

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify...

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candi...

Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity...

Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very ofte...

RNA-Seq data from human semen suggests that the study of the sperm transcriptome requires the previous elimination from the ejaculates of somatic cells carrying a larger load of RNA. Semen purification is also carried to study the sperm transcriptome in other species including swine and it is often done by density gradient centrifugation to obtain...

Background: The mammalian mature spermatozoon has a unique chromatin structure in which the vast majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The chromatin structure of sperm remains unresolved in most livestock species, including the pig...

mir-33a and mir-33b are co-transcribed with the SREBF2 and SREBF1 transcription factors, respectively. The main role of SREBF1 is the regulation of genes involved in fatty acid metabolism, while SREBF2 regulates genes participating in cholesterol biosynthesis and uptake. Our objective was to study the expression of both miR-33a and miR-33b, togethe...

Background Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, the molecular basis of sperm quality is not yet fully understood. Our aim was to identify candidate genes, pathways and DNA variants associated to sperm qua...

Background: The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the leve...

Transmission Ratio Distortion (TRD), the uneven transmission of an allele from a parent to its offspring, can be caused by allelic differences affecting gametogenesis, fertilization or embryogenesis. However, TRD remains vaguely studied at a genomic scale. We sequenced the diploid and haploid genomes of 3 boars from leukocytes and spermatozoa at 50...

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput charac...

The skin microbiota interacts with the host immune response to maintain the homeostasis. Changes in the skin microbiota are linked to the onset and the progression of several diseases, including tumors. We characterized the skin surface and dermal microbiota of 11 dogs affected by spontaneous mast cell tumor (MCT), using skin contralateral sites as...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the leve...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Circular RNAs (circRNAs) are emerging as a novel class of noncoding RNAs which potential role as gene regulators is quickly gaining interest. circRNAs have been studied in different tissues and cell types across several animal species. However, a thorough characterization of the circRNAome in ejaculated sperm remains unexplored. In this study, we p...

Background: Genetic pressure in animal breeding is sparking the interest to select for elite boars with higher sperm quality to maximize ejaculate doses and fertility rates. However, the molecular basis of sperm quality remains largely unexplored. In this study, we sought to identify candidate genes, pathways and DNA variants associated to sperm qu...

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar’s reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, a high throughput characte...

The identification of milk microbial communities in ruminants is relevant for understanding the association between milk microbiota and health status. The most common approach for studying the microbiota is amplifying and sequencing specific hypervariable regions of the 16S rRNA gene using massive sequencing techniques. However, the taxonomic resol...

Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic reso...

The concept that ruminant mammary gland quarters are anatomically and physiologically unrelated has been recently challenged by immunological evidence. How this interdependence reflects on individual quarter milk microbiota is unknown. The aim of the present study was to cover this gap by investigating the interdependence of quarters among the same...

Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to the characterization of the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and deca...

Circular RNAs (circRNAs) are emerging as a novel class of noncoding RNAs which potential role as gene regulators is quickly gaining interest. Although circRNAs have been studied in several tissues and cell types across several animal species, the characterization of the circRNAome in ejaculated sperm remains unexplored. In this study, we profiled t...

Summary statistics of the de novo transcriptome assembly. Summary statistics of the Trinity output based on the number of potential novel genes and transcripts, and size (in bp) of the contigs based on all transcripts isoforms or based only on the longest isoform for each potential gene.

Non-redundant list of genes identified by de novo analysis. 768 potentially novel genes were identified from the unmapped reads. The gene symbol IDs were retrieved with Uniprot from the Trinity output protein names. These genes were detected in at least one species (detailed in column 2 of Supplementary File S8). The majority of these genes were an...

List of long non-coding RNAs detected in porcine sperm. Ensembl IDs of the lncRNAs identified in this study, their genome coordinates, average RNA abundance across the 10 samples and length. Most of the lncRNAs presented, as an average across all samples, low RNA abundances.

RNA abundance levels and coefficient of variation of miRNAs, tRNAs, and piRNAs in the porcine sperm. RNA abundance is measured in CPM (Counts Per Million) across the 10 samples. We only considered the miRNAS with >0 CPMs in all the samples. The genomic coordinates of piRNAs refer to the Sscrofa10.2 built instead of Sscrofa11.1 as provided by the pi...

Novel piRNA clusters identified in the pig sperm RNA. We detected 17 potential clusters of piRNAs that were found in at least 3 of the 10 samples analyzed in this study. Mean and standard deviation (SD) in CPM (Counts Per Million).

RNA-seq quality and mapping statistics. Average and Standard Deviation (SD) for the 10 boar sperm samples processed, including: amount of RNA extracted and several RNA-seq bioinformatics statistics for both total and small RNA-seq.

Distribution of the top decile most abundant SREs (Sperm RNA Elements) into SRE types and gene biotypes. Number of SREs (within the top decile) for each SRE type (exonic, intronic, upstream/downstream 10 kb and orphan). Total non-redundant number of genes and their biotype for each SRE class.

List of human and bovine genes identified by syntenic alignment of the orphan SREs. Orphan SRE genome coordinates were liftover to human and bovine coordinates, and the genes mapped in these regions were extracted. A total of 45 genes shared in both species were found. From these genes, 44 were already annotated in the Sscrofa Ensembl v.91 annotati...

Gene Ontology analysis of the different SRE abundance variance groups. GO biological process terms with significant Bonferroni corrected p-values (p-val < 0.05) and their associated genes.

Concordance of miRNA identification between our dataset and other sperm RNA-seq studies. Comparison of the miRNAs identified in our study with other sperm RNA-seq experiments in pig, in human, and cattle.

Gene Ontology analysis of the genes including the top decile most abundant and the orphan SREs detected in the SRE pipeline. GO biological process terms with significant Bonferroni corrected p-values (p-val < 0.05) and their associated genes.

Correlation between transcript integrity across samples, with transcript abundance and coding sequence length. Correlation of the TIN (Transcripts Integrity Number) between samples, with the transcript abundance and with the coding sequence length of the transcripts. This table shows the correlation of the TIN (Transcripts Integrity Number) between...

List of proteins identified by de novo analysis, with the species in which they were detected and transcript abundance. De novo analysis of the unmapped reads resulted in 1,060 proteins which passed the quality control filters. For each protein, we include the cognate species, the predicted RNA mean abundance in the 10 samples (in FPKM), the Standa...

Distribution of the short RNA-seq reads mapping to different RNA types. Proportion and standard deviation (SD) across the 10 samples.

Water buffalo mastitis represents a major issue in terms of animal health, cost of therapy, premature culling and decreased milk yeld. The emergence of antibiotic resistance has led to investigate strategies to avoid or reduce antibiotics’ based therapies, in particular during subclinical mastitis. The use of Generally Regarded As Safe bacteria (GR...

Relative abundance (> 1%) of microbiota taxa at family level. PBS: quarters treated with sterile PBS only, LAB: quarters treated with inactivated culture of Lactobacillus rhamnosus only, AB: quarters treated with antibiotics, as described in Material and Methods. T0: time zero; T6: time at 6 days post treatment. (DOCX)

Water buffalo milk taxonomic profile at family level (relative abundance of > 1%). PBS: quarters treated with sterile PBS only, LAB: quarters treated with inactivated culture of Lactobacillus rhamnosus only, Ab: quarters treated with antibiotics, as described in Material and Methods. T0: time zero; T6: time at 6 days post treatment. (TIF)

Sampling time, microbiological result, SCC and group for each quarter included in the study. MC: Microbiological count. SCC (Somatic Cell Count) is x 1000. NA: not Assessed. (DOCX)

Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to characterize the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and decays in the s...

Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples often contain DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to as...

Background: Profiling microbiome on low biomass samples is challenging for metagenomics since these samples are prone to present DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to...

Background: African swine fever virus (ASFV) is the etiological agent of African swine fever (ASF), a re-expanding devastating and highly lethal hemorrhagic viral disease. microRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. The discovery of virus specific miRNAs has increased both in nu...

The goal of the current study is to analyse the gene expression profile of the ovine skeletal muscle as well as to characterize the genetic variation of transcripts expressed in such tissue. This aim has been achieved by sequencing the longissimus dorsi transcriptomes of 50 sheep distributed in five pools representing the Canaria de Pelo, Roja Mall...

Myobia sp. and Demodex sp. are two skin mites that infest mice, particularly immunodeficient or transgenic lab mice. In the present study, wild house mice from five localities from the Barcelona Roberstonian system were analysed in order to detect skin mites and compare their prevalence between standard (2n = 40) and Robertsonian mice (2n > 40). We...

Abbreviations: FPKM: fragments per kilobase of transcript per million mapped reads; KRT1: keratin 1; miRNA: micro-RNA; miscRNA: miscellaneous RNA; Mt rRNA: mitochondrial ribosomal RNA; Mt tRNA: mitochondrial transference RNA; OAZ3: ornithine decarboxylase antizyme 3; ORT: osmotic resistance test; piRNA: Piwi-interacting RNA; PRM1: protamine 1; PTP...

Background: The individual, together with its environment, has been reported as the main force driving composition and structure of skin microbiota in healthy dogs. Therefore, one of the major concerns when analyzing canine skin microbiota is the likely influence of the environment. Despite the dense fur covering, certain skin diseases exhibit dif...