论文主要研究内容及重要结论: The transcriptome data analyses provided high quality data with 95.36% alignment to reference genome and revealed 34.57% (5574) novel genes, where 55.58% (3,999) were up-regulated and 44.41% (3,195) down-regulated. Additionally, 138 (42 up-regulated and 14 down-regulated) and 133 (57 up-regulated and 42 down-regulated) transcripts belonging to HSP and FN-III proteins, respectively were also revealed. Moreover, 2076 housekeeping genes including 24 novel transcripts, 199 up-regulated, 344 down-regulated, and 1533 normal transcripts were also identified. The functional annotation revealed that DEGs, HSPs, FN-III proteins, and housekeeping gene were associated with cellular metabolic activities, signal transduction, cytoprotection, structural and binding activities. The related functional pathways included cancer pathway, PI3k-Akt signaling, axon guidance, adhesion, and regulation of actin cytoskeleton, JAK-STAT signaling, basic cellular metabolism, disease regulation, thermogenesis, and oxidative phosphorylation. For the first time, our study provides considerable deep understanding of transcriptomic data (brain vs non-brain tissues) including DEGs, HSPs, FN-III proteins, and housekeeping genes having potential role in basic cellular activities and the neural development of swamp buffalo that ultimately helped to maintain their working capacity and social interaction with humans. Through comparative genomic, evolutionary and transcriptome analyses, the present study provides an evolutionary and molecular level insight into the characterization of HSPs and FN-III proteins gene families in buffalo owing to their functional importance. A total of 64 and 29 genes of HSP and FN-III proteins, were widely dispersed across the buffalo genome. In buffalo, phylogenetic relationship, motif, and conserved domain analyses demonstrated that all the members of HSP and FN-III protein gene families are well conserved with a variety of stable to unstable, hydrophobic to hydrophilic, and thermostable to thermo-unstable proteins nature. The HSP90 gene family of buffalo is more conserved in nature as compared to the HSP70 family that exhibited a quite higher ratio of non-synonymous substitutions. Structural variations in secondary structures of HSP40 and HSP90 were observed in buffalo and cattle. Moreover, comparative structural configuration for FNDC5 predicted variable amino acid residues but the FNDC5 structure for human, Mediterranean buffalo, and Bos taurus was similar to each other. The predicted binding scores and interface residues of FNDC5/irisin as a ligand for representative receptors, presented functional role for energy homeostasis and significant involvement in the folliculogenesis and spermatogenesis in the buffalo.The findings of the present study provide insights into the genomic and evolutionary attributes of HSP and FN-III protein gene families, which would definitely help to better understand crucial functions of these genes and their potential contribution/utility for selective breeding of buffalo for better thermotolerance, stress resilience, energy homeostasis, folliculogenesis and spermatogenesis. Furthermore, the transcriptomic data analyzed in the present study would not only help to elucidate the genetic architecture of different phenotypic traits but also regulation of their gene expression in the buffalo. |
论文的创新点内容：For the first time, our study provides considerable deep understanding of transcriptomic data (brain vs non-brain tissues) including DEGs, HSPs, FN-III proteins, and housekeeping genes having potential role in basic cellular activities and the neural development of swamp buffalo that ultimately helped to maintain their working capacity and social interaction with humans. Moreover, the transcriptomic data analyzed in the present study would not only help to elucidate the genetic architecture of different phenotypic traits but also regulation of their gene expression in the buffalo. Through comparative genomic, evolutionary and transcriptome analyses, the present study provides an evolutionary and molecular level insight into the characterization of HSPs gene families in buffalo owing to their functional importance. The genomic variations in the HSP gene families could be used for a better understanding of the function of these genes and their further use for selective breeding of buffalo for better thermotolerance and stress resilience. The is the preliminary study in buffalo that presented the molecular structure and function of FN-III genes family demonstrated their evolutionary conserved nature with diverse physiochemical properties. Further, we predicted the binding scores and interface residues of FNDC5/irisin as a ligand for six representative receptors, with functional role for energy homeostasis and significant involvement in folliculogenesis and spermatogenesis in the buffalo. These findings would definitely help to better understand crucial functions of these genes and their potential contribution/utility for selective breeding of buffalo for better energy homeostasis, folliculogenesis and spermatogenesis. |
