Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan

Saleem, Farrukh; Ameer, Aqsa; Star-Shirko, Banaz; Keating, Ciara; Gundogdu, Ozan; Ijaz, Umer Zeeshan; Javed, Sundus

Abstract

This article focuses the recovery of prokaryotic organisms including bacteria and archaea from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise of three different breeds (Broilers, White Layers, and Black Australorp) of chicken raised in different farming setups that include antibiotic-free control, commercial (open and controlled shed), and backyard farms. We have recovered 569 Metagenomics-Assembled Genomes (MAGs) with a completeness of ≥50% and contamination of ≤10%. For each MAG, functional annotations were obtained that include KEGG modules, carbohydrate active enzymes (CAZymes), peptidases, geochemical cycles, antibiotic resistance genes, stress genes, and virulence genes. Furthermore, two different sets of Single Copy Genes (SCGs) were used to construct the phylogenetic trees. Based on the reconstructed phylogeny, phylogenetic gain of each MAG is calculated to give an account of novelty.

Citation

Saleem, F., Ameer, A., Star-Shirko, B., Keating, C., Gundogdu, O., Ijaz, U. Z., & Javed, S. (2024). Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data in Brief, 54, Article 110552. https://doi.org/10.1016/j.dib.2024.110552

• Journal Article Type: Article
• Acceptance Date: May 18, 2024
• Online Publication Date: May 23, 2024
• Publication Date: May 23, 2024
• Deposit Date: Jun 10, 2024
• Publicly Available Date: Jun 10, 2024
• Journal: Data in Brief
• Electronic ISSN: 2352-3409
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 54
• Article Number: 110552
• DOI: https://doi.org/10.1016/j.dib.2024.110552
• Public URL: https://durham-repository.worktribe.com/output/2471639