Ontology highlight
ABSTRACT:
PROVIDER: PRJNA951806 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24057900_1.fastq.gz | Fastqsanger.gz | |||
| SRR24057900_2.fastq.gz | Fastqsanger.gz | |||
| SRR24057901_1.fastq.gz | Fastqsanger.gz | |||
| SRR24057901_2.fastq.gz | Fastqsanger.gz | |||
| SRR24057902_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Bubalus bubalis breed:Water buffalo Genome sequencing
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Project description:The domestic buffalo (Bubalus bubalis) has presented an important role in the livestock industry, contributing to milk and meat production worldwide, especially in developing countries. However, little is known about its reproductive particularities. Studies regarding protein composition of buffalo SP are still limited and a complete mapping of buffalo SP proteins is still lacking in the literature. Hence, a comprehensive study of SP proteome is of great importance to better understand the mechanisms involved in male reproduction and to optimize the reproductive biotechnologies of farm animal species. Therefore, the aim of this study is to describe for the first time the Bubalus bubalis seminal plasma proteome using a label free shotgun HDMS approach. This type of analysis is interesting since it yields a high number of detected proteins, generating a dataset that is useful for further characterizing the buffalo SP.
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Project description:Protein ubiquitination, a major and conserved post-translational modification, is known to play a critical regulatory role in many biological processes in eukaryotes. Although several ubiquitinated proteins have been found in buffalo (Bubalus bubalis) testis in our previous studies, large-scale profiling of buffalo testis ubiquitome has not been reported to date. In this study, we firstly identified a global profiling of lysine ubiquitination of adult buffalo testis using a highly sensitive LC-MS/MS coupled with immune-affinity enrichment of ubiquitinated peptides. In total, 422 lysine ubiquitination sites were identified in 262 proteins in adult buffalo testis tissue. Bioinformatic analysis showed that the ubiquitinated proteins are involved in a variety of biological processes and diverse subcellular localizations. Besides, KEGG pathway and protein interaction network analysis indicated that proteasome, glycolysis/gluconeogenesis and gap junction pathways are modulated by protein ubiquitination in testis. Taken together, these data provide a global view of ubiquitome in buffalo testis for the first time, and serve as an important resource for exploring the physiological role of lysine ubiquitination in testis in mammalian.
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Project description:Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and histone modifications. During spermatogenesis, the DNA of sperm undergoes overall methylation changes and this could have some role to play in fertilizing ability of the sperm. Many of the studies have shown that the altered methylation can cause sub fertility. In the present study we report the development of first comprehensive 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray for studying the global DNA methylation profile of buffalo sperm. The array has been developed by employing microarray based comparative genomic hybridization (aCGH) technique with bovine and buffalo DNA using bovine genome sequence as reference. The array represents 157084 features assembled from CDS, Promotor and CpG regions covering 2,967 unique genes. We also report the comparison of genome wide methylation differences in buffalo sperm from high fertile and sub fertile bulls which indicated profound discrepancies in their methylation status. A total of 96 individual genes along with another 55 genes covered under CpG islands were found differentially methylated and and were associated with different cellular functions and biological processes affecting germ cell development, spermatogenesis, capacitation and embryonic development.
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