Genome-wide identification and expression analysis of the Collagen family during lactation in water buffalo (Bubalus Bubalis)

Abstract Background: Collagens, as extracellular matrix molecules, support cells for structural integrity and a variety of other functions, thereby contribute to support mammary basic structure and development. However, little information on the identification and expression profiles in response to the mammary gland of the collagen family in buffalo (Bubalus Bubalis) has been reported. Results: A total of 128 buffalo collagen protein sequences corresponding to 45 collagen genes were identified and classified into six clusters based on their phylogenetic relationships, conserved motifs, and gene structure analyses. A transcription factor binding sites (TFBS) analysis inferred that a total of 142 TFBS were predicted within the buffalo collagens, suggesting that different collagen subfamilies harbored different TFBS and played a variety of functions involved in the mammary gland development and lactation. The identified collagen sequences were unequally distributed on 17 chromosomes, 103 of which were determined to be tandem duplicated genes. Transcriptome data and qRT-PCR analysis revealed the expression diversity of buffalo collagen genes in various tissues. Most of the identified collagen genes were significantly up-regulated at the early lactation, 6 collagens upregulated at the peak lactation, and only COL24A1 was up-regulated at the late lactation. Conclusions: The present study provides significant insights into the potential functions of collagen family in dairy buffalo and helps in the functional characterization for collagen genes in further research.