BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis.

Abstract

Amidst the global challenge of extreme poverty, the livestock sector can significantly contribute to global sustainable development goals by enhancing resilience, smallholder productivity, and market participation. The Indian livestock sector is one of the largest in the world with a total livestock population of 535.82 million, ∼10.7% of the world's livestock population. Buffalo (Bubalus bubalis) holds significant importance in India and other Asian countries, notably contributing to their economies by surpassing cattle in milk production and providing various valuable products. The limited availability of genomic and transcriptomic resources for buffaloes hinders the efforts to enhance their traits for increased milk and meat production. To address this gap, this study adopted the state-of-the-art bioinformatics tools to analyse 2429 transcriptomes representing 438 BioSamples from 23 BioProjects obtained from a public domain database, representing 76 different types of tissues and cell types from all major organ systems in buffalo species (river and swamp). The outcome of this exhaustive genomic data led to the development of a relational buffalo expression database based on a three-tier architecture named as BuffExDb (http://46.202.167.198/buffex/). The user-friendliness and flexibilities in retrieval of tissue-specific genes (TSGs) and their functional annotation are the major characteristics of BuffExDb. This is the first of its kind that offers an effortlessly navigable and filterable database, enabling users to examine and visualize the expression levels of each tissue across multiple samples, simultaneously. It also provides the Tau score parameter for the identification of TSGs along with their essential roles in tissue development, maintenance, and function as observed through the enrichment test for gene ontologies. The exhaustive outcome of this work would pave the way for the biological, functional, and evolutionary studies for easy access. This prior information based on tissue-specific mechanisms can be used for future genomic research, especially in association studies in endeavour of enhanced buffalo breeding and conservation programmes. Database URL: http://46.202.167.198/buffex/.