Investigating the role of FOX gene family in development and stress response in Labeo rohita: A multi-faceted analysis of phylogeny and genome characterization

Abstract

The forkhead box (FOX) gene family of transcription factors regulates muscle development, immune responses, and metabolic processes across species. Despite extensive studies on FOX genes in other organisms, their evolutionary and functional roles in Labeo rohita, an economically and ecologically important freshwater fish, remain unclear. Owing to its unique physiological and ecological traits, L. rohita is an ideal model for exploring these roles. Here, we present the first computational analysis of the FOX gene family in L. rohita, identifying 21 FOX genes. Physicochemical analysis revealed that most FOX proteins have a basic nature except for FOX A3, D3, I2, O1, O3, O4, P1, and P2. Instability index analysis indicated that all FOX proteins are unstable (values > 40), while hydrophobicity assessment showed that except FOX O1, all proteins are hydrophobic. Phylogenetic analysis grouped FOX homologs into 11 major clades with other vertebrates. All proteins exhibited structural homogeneity by sharing the Forkhead Box domain. Gene structure comparisons revealed seven duplicated pairs, and Circos analysis demonstrated organization into 20 clusters. This study highlights the critical roles of FOX genes and fills a significant knowledge gap, providing a foundation for future functional and phylogenomic studies with implications for aquaculture and evolutionary biology.

Fig 1. Phylogenetic tree of the FOX gene superfamily based on 94 amino acid sequences from five species (L. rohita, O. niloticus, C. idella, D. rerio, and H. sapiens), clustering into 11 clades.

Fig 2. Structural Analysis of the FOX gene superfamily: (A) Phylogenetic tree, (B) Motifs, (C) Domains, and (D) Gene structure in L. rohita.

Fig 3. Syntenic relationships between FOX genes in L. rohita and H. sapiens.

The gray lines in the background depict collinear blocks in the genomes of L. rohita and H. sapiens, while the red lines emphasize the syntenic pairs of FOX genes.

Fig 4. Illustration of FOX superfamily gene localization and duplication events.

(A) The positions of FOX genes across all 12 chromosomes of L. rohita are shown, with mega-bases (Mb) used as the scale on the left. The corresponding chromosomal numbers are indicated at the center of each bar. (B) A Circos plot depicts the FOX genes in the L. rohita genome, highlighting gene duplication events. Duplicated regions are shown in proximity due to the arrangement of the chromosomes, with segmentally duplicated genes connected by a direct communication pathway.

Fig 5. Three-dimensional structure of the FOX gene superfamily in L. rohita generated using Phyre2.

Fig 6. Scan PROSITE identified intra-domain predictions.

This image represents all detected features and matches of the specified type. Pattern hits are displayed as thin colored bars without text, while hit profiles are represented as colored shapes accompanied by their corresponding PROSITE names.