Biology subjects

Gonzalez-Recio, O.

Publications and source records attributed to Gonzalez-Recio, O..

6 recordsLinked to original sources

bioRxiv2025

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

BackgroundDNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. ResultsManufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The EpiChip has demonstrated a good ability to explore biological processes such as genomic imprinting and differences between cell types, opening the possibility of inferring blood cell composition. Finally, analysis of longitudinal ear biopsies allowed accurate age prediction, suggesting the potential of the array to refine epigenetic clocks. ConclusionsThe RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.

genomics↗

bioRxiv2025

Unveiling the hidden biodiversity of microbial chemoreceptor genes in the rare biosphere

Chemoreception plays a central role in microbial adaptability, influencing both community structure and interactions with the environment. However, many chemosensitive microorganisms occur at low abundances in natural ecosystems, which has limited their detection and study using conventional metagenomic sequencing. Here, we employed a custom-designed target capture sequencing approach--encompassing all known chemoreceptor genes from both cultured and uncultured microorganisms--to uncover and characterize the vast chemosensory potential and biodiversity within the rarest fractions of the microbiome. Compared to standard environmental sequencing methods, our approach enhanced the detection of chemoreceptor (CR) genes and their associated sensing domains by orders of magnitude across diverse environments, including the rhizosphere, phyllosphere, soil, aquatic ecosystems, the human gut, and bovine rumen. This enabled the identification of thousands of low-abundance chemosensitive microorganisms that remained undetectable using conventional sequencing approaches, including known plant pathogens and symbionts. Phylogenetic analysis of the most divergent CR genes revealed evidence for novel chemosensitive species, potentially representing new bacterial phyla and classes. Our study provides a new perspective on the chemoreception capabilities of environmental microbes and opens new avenues for discovering and characterizing novel microbial sensing mechanisms.

microbiology↗

bioRxiv2023

Accuracy of direct genomic values and methylation profile through genotype-by-LowPass sequencing using Nanopore technology

Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome. It requires a low sequencing depth to be cost effective, which may increase the error at the genotype assigment. Third generation Nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation, which provides added value to genotype-by-sequencing. The aim of this study was to evaluate the performance of genotype-by-LowPass Nanopore sequencing for estimating the direct genomic value in dairy cattle, and the possibility to obtain methylation marks simultaneously. Latest Nanopore chemistry (LSK14 and Q20) achieved a modal base calling accuracy of 99.55 %, whereas previous kit (LSK109) achieved slightly lower accuracy (99.1 %). The direct genomic value accuracy from genotype-by-Low Pass sequencing ranged between 0.79 and 0.99, depending on the trait, with a sequencing depth as low as 2x and using the latest chemistry (LSK114). Lower sequencing depth led to biased estimates, yet with high rank correlations. The LSK109 and Q20 achieved lower accuracies (0.57-0.93). More than one million high reliable methylated sites were obtained, even at low sequencing depth, located mainly in distal intergenic (87 %) and promoter (5 %) regions. This study showed that the latest Nanopore technology can be use in a LowPass sequencing framework to estimate direct genomic values with high reliability. It may provided advantages in populations with no available SNP chip, or when a large density of markers with a wide range of allele frequencies is needed. In addition, Low Pass sequencing provided with nucleotide methylation status of >1 million nucleotides at [≥] 10x, which is an added value for epigenetic studies.

genomics↗

bioRxiv2021

Sequencing of Sars-CoV-2 genome using different Nanopore chemistries

Nanopore sequencing has emerged as a rapid and cost-efficient tool for diagnostic and epidemiological surveillance of SARS-CoV-2 during the COVID-19 pandemic. This study compared results from sequencing the SARS-CoV-2 genome using R9 vs R10 flow cells and Rapid Barcoding Kit (RBK) vs Ligation Sequencing Kit (LSK). The R9 chemistry provided a lower error rate (3.5%) than R10 chemistry (7%). The SARS-CoV-2 genome includes few homopolymeric regions. Longest homopolymers were composed of 7 (TTTTTTT) and 6 (AAAAAA) nucleotides. The R10 chemistry resulted in a lower rate of deletions in timine and adenine homopolymeric regions than R9, at expenses of a larger rate (~10%) of mismatches in these regions. The LSK had a larger yield than RBK, and provided longer reads than RBK. It also resulted in a larger percentage of aligned reads (99% vs 93%) and also in a complete consensus genome. The results from this study suggest that the LSK used on a R9 flow cell could maximize the yield and accuracy of the consensus sequence when used in epidemiological surveillance of SARS-CoV-2. KeypointsO_LISequencing SARS-CoV-2 genome is of great importance for the pandemic surveillance C_LIO_LINanopore offers a low cost and accurate method to sequence SARS-CoV-2 genome C_LIO_LILigation sequencing is preferred rather than the rapid kit using transposases C_LI

microbiology↗

bioRxiv2019

Long reads from Nanopore sequencing as a tool for animal microbiome studies

In the era of bioinformatics and metagenomics, the study of the ruminal microbiome has gained considerable relevance in the field of animal breeding, since the composition of the rumen microbiota significantly impacts production and the environment. Illumina sequencing is considered the gold standard for the analysis of microbiomes, but it is limited by obtaining only short DNA sequences to analyze. As an alternative, Oxford Nanopore Technologies (ONT) has developed a new sequencing technique based on nanopores that can be carried out in the MinION, a portable device with a low initial cost which long DNA readings can be obtained with. The aim of this study was to compare the performance of both types of sequencing applied to samples of ruminal content using a similar pipeline. The ONT sequencing provided similar results to the Illumina sequencing, although it was able to classify a greater number of readings at the species level, possibly due to the increase in the read size. The results also suggest that, due to the size of the reads, it would be possible to obtain the same amount of information in a smaller number of hours. However, detection of archaeal and eukaryotic species is still difficult to accomplish due to their low abundance in the rumen compared to bacteria, suggesting different pipelines and strategies are needed to obtain a whole representation of the less abundant species in the rumen microbiota.

microbiology↗

bioRxiv2017

Signs of host genetic regulation in the microbiome composition in cattle

Previous studies have revealed certain genetic control by the host over the microbiome composition, although in many species the host genetic link controlling microbial composition is yet unknown. This potential association is important in livestock to study all factors and interactions that rule the effect of the microbiome in complex traits. This report aims to study whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Data on 16S and 18S rRNA gene-based analysis of the rumen microbiome in 18 dairy cows from two different breeds (Holstein and Brown Swiss) were used. The effect of the genetic background of the animal (through the breed and Single Nucleotide Polymorphisms; SNP) on the relative abundance (RA) of archaea, bacteria and ciliates (with average relative abundance per breed >0.1%) was analysed using Bayesian statistics. In total, 13 genera were analysed for bacteria (5), archaea (1), and ciliates (7). All these bacteria and archaea genera showed association to the host genetic background both for breed and SNP markers, except RA for the genera Butyrivibrio and Ruminococcus that showed association with the SNP markers but not with the breed composition. Relative abundance of 57% (4/7) of ciliate analysed showed to be associated to the genetic background of the host. This host genetic link was observed in some genus of Trichostomatia family. For instance, the breed had a significant effect on Isotricha, Ophryoscolex and Polyplastron, and the SNP markers on Entodinium, Ophryoscolex and Polyplastron. In total, 77% (10/13) of microbes analysed showed to be associated to the host genetic background (either by breed or SNP genotypes). Further, the results showed a significant association between DGAT1, ACSF3, AGPAT3 and STC2 genes with the relative abundance Prevotella genus with a false discovery rate lower than 15%. The results in this study support the hypothesis and provide some evidence that there exist a host genetic component in cattle that can partially regulate the composition of the microbiome.

genomics↗