Biology subjects

Moreira, G. C. M.

Publications and source records attributed to Moreira, G. C. M..

3 recordsLinked to original sources

bioRxiv2024

Empowering bioinformatics communities with Nextflow and nf-core

Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line solutions such as Nextflow and Snakemake. We report on recent developments in the nf-core and Nextflow frameworks that have led to widespread adoption across many scientific communities. We describe how adopting nf-core standards enables faster development, improved interoperability, and collaboration with the >8,000 members of the nf-core community. The recent development of Nextflow Domain-Specific Language 2 (DSL2) allows pipeline components to be shared and combined across projects. The nf-core community has harnessed this with a library of modules and subworkflows that can be integrated into any Nextflow pipeline, enabling research communities to progressively transition to nf-core best practices. We present a case study of nf-core adoption by six European research consortia, grouped under the EuroFAANG umbrella and dedicated to farmed animal genomics. We believe that the process outlined in this report can inspire many large consortia to seek harmonisation of their data analysis procedures.

bioinformatics↗

bioRxiv2023

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing

Understanding the genomic control of tissue-specific gene expression and regulation can help to inform the application of genomic technologies in farm animal breeding programmes. The fine mapping of promoters (transcription start sites [TSS]) and enhancers (divergent amplifying segments of the genome local to TSS) in different populations of cattle across a wide diversity of tissues provides information to locate and understand the genomic drivers of breed- and tissue-specific phenotypes. To this aim we used Cap Analysis Gene Expression (CAGE) sequencing to define TSS and their co-expressed short-range enhancers (<1kb) in the ARS-UCD1.2_Btau5.0.1Y reference genome (1000bulls run9) and analysed tissue- and population specificity of expressed promoters. We identified 51,295 TSS and 2,328 TSS-Enhancer regions shared across the three populations (Holstein, Charolais x Holstein and Kinsella beef composite [KC]). In addition, we performed a comparative analysis of our cattle dataset with available data for seven other species to identify TSS and TSS-Enhancers that are specific to cattle. The CAGE dataset will be combined with other transcriptomic information for the same tissues generated in the BovReg project to create a new high-resolution map of transcript diversity across tissues and populations in cattle. Here we provide the CAGE dataset and annotation tracks for TSS and TSS Enhancers in the cattle genome. This new annotation information will improve our understanding of the drivers of gene expression and regulation in cattle and help to inform the application of genomic technologies in breeding programmes.

genomics↗

bioRxiv2018

Association of predicted deleterious single nucleotide polymorphisms with carcass traits in meat-type chickens

In previous studies, we used genome wide association (GWAS) to identify quantitative trait loci (QTL) associated with weight and yield of abdominal fat, drumstick, thigh and breast traits in chickens. However, this methodology assumes that the studied variants are in linkage disequilibrium with the causal mutation and consequently do not identify it. In an attempt to identify causal mutations in candidate genes for carcass traits in broilers, we selected 20 predicted deleterious SNPs within QTLs for association analysis. Additive, dominance and allele substitution effects were tested. From the 20 SNPs analyzed, we identified six SNPs with significant association (p-value <0.05) with carcass traits, and three are highlighted here. The SNP rs736010549 was associated with drumstick weight and yield with significant additive and dominance effects. The SNP rs739508259 was associated with thigh weight and yield, and with significant additive and allele substitution effects. The SNP rs313532967 was associated with breast weight and yield. The three SNPs that were associated with carcass traits (rs736010549, rs739508259 and rs313532967) are respectively located in the coding regions of the WDR77, VWA8 and BARL genes. These genes are involved in biological processes such as steroid hormone signaling pathway, estrogen binding, and regulation of cell proliferation. Our strategy allowed the identification of putative casual mutations associated with muscle growth.

genetics↗