Project description:Duplicated sequences are the important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we estimated 44.6 Mb (~1.73% of cattle genome) segmental duplications in the autosomes and X chromosome using the sequencing reads of Olimpia (the sequenced water buffalo). 70.3% (70/101) duplications were experimentally validated using the fluorescent in situ hybridization. We also detected a total of 1344 CNV regions across 14 additional water buffalos as well as Olimpia, amounting to 59.8Mb of variable sequence or 2.2% of the cattle genome. The CNV regions overlap 1245 genes and are significantly enriched for specific biological functions such as immune response, oxygen transport, sensory system and signalling transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffalos as test samples and Olimpia as the reference. Using a linear regression model, significant and high Pearson correlations (r = 0.781) were observed between the digital aCGH values and aCGH probe log2 ratios. We further designed Quantitative PCR assays to confirm CNV regions within or near annotated genes and found 74.2% agreement with our CNV predictions.
Project description:To investigate microRNAs (miRNAs) involving in the regulation of the schistosome development and survival, we compared miRNA expression profiles of adult Schistosoma japonicum derived from yellow cattle and water buffalo using high-throughput sequencing with Illumina Hiseq Xten.
Project description:Trypanosoma (Megatrypanum) theileri is a ubiquitous parasite of Bovinae (cattle, buffalo, yaks and some antelopes). Here were report the transcriptome sequence of this parasite
Project description:Fasciola gigantica infects buffalo in Asian and African countries and causes significant economic losses. As a kind of zoonotic parasite disease, human infection has been reported and make fascioliasis patients suffer heavy abdominal pain, anemia and workforce loss. Fasciola can modulate host immune responses to survive from immune attack and some mechanisms have been reported with its antigen protein. Protein, as the chief actors within the cell, presents the dynamic changes of body with its specific changes and serves as unexceptionable biomarkers in many disease-detections. But there is not any study about serum proteomic for diagnostic target seeking in buffalo after infection with F. gigantica. Herein, Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) and Parallel Reaction Monitoring (PRM) technologies were used in the present study to reveal the dynamic changes of proteins in buffalo serum after infected with F. gigantica. Six proteins were found significantly regulated in all three groups which reminds us that they could be used as new diagnostic biomarkers in buffalo throughout F. gigantica infection. All these are new findings in buffalo after infection with F. gigantica and could provide a new insight into the potential possibility in this parasite clearance.
