A Genome-Wide Identification and Analysis of the Basic Helix-Loop-Helix Transcription Factors in Water Buffalo (Bubalus bubalis)

Background: Water buffalo (Bubalus bubalus) are domesticated animals of economic importance in many Asian countries, whereas the basic helix-loop-helix (bHLH) transcription factors (TFs) have been analyzed in the genomes of many eukaryote organisms. However, the bovine bHLH TFs have not been characterized and their specific functions remain unknown. Objective: To better characterize and functionally understand the bovine bHLH TFs, we systematically analyzed and characterized putative bHLH proteins in the ongoing genome project of water buffalo. Method: We carried out multiple BLAST searches, phylogenetic analysis, conserved site analysis, enrichment analyses of gene ontology and pathway annotations, and other functional annlyses with KOBAS, Blast2GO, and DAVID Bioinformatics Resources. Results: Among the identified 105 bHLH TFs, phylogenetic analyses classified 103 bHLH TFs into 43 families with 60, 77, 25, 20, and 9 protein sequences in the higher-order groups A, B, C, E and F, respectively. The remaining 8 protein sequences of 3 putative bHLH TFs were categorized as “orphan proteins” and annotated as SOHLH2, MGA, and TCFL5. Furthermore, these bovine bHLH proteins were characterized as significantly enriched in 361 significant (corrected P value ≤ 0.05) and 215 very significant (corrected P value ≤ 0.001) Gene Ontology (GO) annotations as well as 18 significantly (corrected P value ≤ 0.05) and 12 very significant (corrected P value ≤ 0.001) enriched cellular pathways and other categories. Conclusion: The present research provides new data and a good reference for further functional and evolutionary investigations on mammalian development using water buffalo as a model animal.