Male buffalo genome sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB58214 | ENA |
REPOSITORIES: ENA
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Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.
2019-12-20 | GSE123869 | GEO
Project description:Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Six small RNA libraries were constructed. A total of 66,128,645 and 70,974,347 raw reads were obtained from muscle and adipose groups, respectively. After filtering the adaptor and low quality reads, 60,765,257 and 67,327,095 clean reads were retained. In total, 721 miRNAs were identified.
2021-08-27 | GSE119064 | GEO
Project description:Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Three small RNA libraries were constructed. A total of 32762032 raw reads were obtained from adipose groups, respectively. After filtering the adaptor and low quality reads, 32054381 clean reads were retained. In total, 623 miRNAs were identified.
2021-12-31 | GSE171146 | GEO
Project description:Spermatogenesis carries the task of precise intergenerational transmission of genetic information from the paternal genome and involves complex developmental processes regulated by the testicular microenvironment. Studies performed mainly in mouse models have established the theoretical basis for spermatogenesis, yet the wide inter-species differences preclude direct translation of the findings, and farm animal studies are progressing slowly. More than 32,000 cells from prepubertal (3-month-old) and pubertal (24-month-old) buffalo testes were analyzed using single-cell RNA sequencing (scRNA-seq), and dynamic gene expression roadmaps of germ cell and somatic cell development were generated. In addition to identifying the dynamic processes of sequential cell fate transitions, the global cell-cell communication essential to maintain regular spermatogenesis in the buffalo testicular microenvironment was uncovered. The findings provide the theoretical basis for establishing buffalo germline stem cells in vitro or culturing organoids and facilitating the expansion of superior livestock breeding.
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Project description:Buffalo breeding has become an important branch of beef cattle industry. It is of great significance to study buffalo meat production and meat quality. However, the important role of mRNA and lncRNA molecules in muscle stem cells (MuSCs) development in buffalo has not been explored. Then, we performed mRNA and lncRNA expression profiling analysis on the proliferation and differentiation of MuSCs in buffalo. The results showed that there were 4,820 differentially genes, 12,227 mRNAs, and 1,352 lncRNAs. These differentially expressed mRNAs are enriched in biological processes such as cell cycle, p53 signaling pathway, RNA transport, and Calcium signaling pathway and others. We also identified a number of genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the role of mRNA and lncRNA expression in the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.
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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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