The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility. ViSEAGO is publicly available on https://bioconductor.org/packages/ViSEAGO .

The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum. Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions. This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.

Phosphorus (P) is an essential mineral in poultry nutrition, but its low bioavailability from conventional feed ingredients presents a significant challenge for efficient utilization. This study investigated the effects of different P sources (monocalcium phosphate (MCP) and calcium humophosphate (CHP)) and three phytase concentrations (0, 1000, or 2000 FTU/kg of feed) on broiler performance and ileal nutrient digestibility. A total of 600 Cobb 500 male broilers were fed one of six different dietary treatments with 10 replicates per treatment from 11 to 21 d of age. The birds and feed were weighed at 1, 10, and 21 d of age to determine growth performance. At 21 d of age, ileal digesta was collected from all the birds to determine dry matter, organic matter, Ca, P, and ash digestibility. The results indicated that phytase supplementation at 1000 and 2000 FTU/kg improved the feed conversion ratio and P digestibility compared with the non-supplemented group. The broilers fed CHP showed superior P digestibility compared to those fed MCP, regardless of phytase concentration. The results also indicated interactive effects between P source and phytase concentration on the digestibility of dry matter, organic matter, and ash. The findings suggest that CHP enhances nutrient digestibility and could optimize P utilization in broiler diets with phytase inclusion. This report reveals a better understanding of the effects of P sources and phytase concentration on feed digestibility. Further studies are needed to confirm these findings and support improvements in broiler performance under commercial production conditions.