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Improved de novo Genomic Assembly for the Domestic Donkey

ABSTRACT: This study aims at improving the genome reference of the domestic donkey using the Chicago/HiRiSe technology.

PROVIDER: PRJEB24845 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2286910_1.fastq.gz	Fastqsanger.gz
	ERR2286910_2.fastq.gz	Fastqsanger.gz
	ERR2286911_1.fastq.gz	Fastqsanger.gz
	ERR2286911_2.fastq.gz	Fastqsanger.gz
	ERR2286912_1.fastq.gz	Fastqsanger.gz

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Improved de novo genomic assembly for the domestic donkey.

Project description:Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

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Donkey Milk

Project description:Donkey Milk Metagenome

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Single-Cell RNA Sequencing unveils dynamic transcriptional profiles during the process of donkey spermatogenesis and maturation

Project description:With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.In this study, we constructed a single-cell RNA dataset to study the single-cell landscape of donkey spermatogenesis and maturation. This method allows us to analyze the cell composition in testicular and epididymal tissue, providing insights into the changes that occur during donkey spermatogenesis and maturation. In addition, different gene expression signatures associated with various spermatogenic cell types were found

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Project description:Donkey milk (DM) has been considered a valuable alternative to human and bovine coun-terparts as well as to infant formulas. Milk extracellular vesicles (EVs) have been proposed to influence key biological processes. The purpose of this study is to provide a compre-hensive characterization of the protein composition of extracellular vesicles (EVs) by ex-tending quantitative proteomic comparisons to EVs derived from donkey colostrum (DC) and mature donkey milk (MDM). The EVs were isolated from DC and MDM samples, characterized, and subjected to proteomic analysis using the tandem mass tag-based quantitative approach

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Zearalenone exposure enhanced the expression of tumorigenesis genes in donkey granulosa cells via the PTEN/PI3K/AKT signaling pathway

Project description:We investigated the biological effects of ZEA exposure on donkey granulosa cells by using RNA-seq analysis. ZEA at 10 and 30 μM were administered to granulosa cells within 72 hours of in vitro culture. ZEA at 10 μM significantly altered the tumorigenesis associated genes in donkey granulosa cells. Exposure to 10 and 30 μM ZEA treatment significantly reduced mRNA expression of PTEN, TGFβ, ATM, and CDK2 genes, particularly, the ZEA treatment significantly increased the expression of PI3K and AKT genes. Furthermore, immunofluorescence, RT-qPCR, and Western blot analysis verified the gene expression of ZEA-exposed granulosa cells. Collectively, these results demonstrated the deleterious effect of ZEA exposure on the induction of ovarian cancer related genes via the PTEN/PI3K/AKT signaling pathway in donkey granulosa cells in vitro.

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Metagenomic sequence of donkey

Project description:Metagenomic sequence of donkey

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Identification and comparative analysis of long non-coding RNA in the skeletal muscle of two Dezhou donkey strains (Equus asinus)

Project description:In this study, 3,869 donkey skeletal muscle lncRNAs were identified using RNA-Seq along with a stringent screening procedure in the longissimus dorsi (LD) and gluteal (G) muscles. These lncRNAs share many characteristics with other mammalian lncRNAs, such as shorter open reading frames (ORFs) and lower expression levels than mRNAs. Furthermore, in pairwise comparisons between libraries of the same stage for two genetic types of male Dezhou donkey, 73 differentially expressed lncRNAs were common to all muscle tissues.

2021-05-24 | GSE128713 | GEO

Donkey orchid symptomless virus

Project description:Donkey orchid symptomless virus Genome sequencing

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Site-specific glycosylation of donkey milk lactoferrin investigated by High Resolution Mass Spectrometry

Project description:A comprehensive glycosylation profile of donkey lactoferrin, isolated by ion exchange chromatography from an individual milk sample, was obtained by means of chymotryptic digestion, TiO2 and HILIC enrichment, reversed-phase high performance liquid chromatography, electrospray mass spectrometry, and high collision dissociation fragmentation. The results obtained allowed the identification of 26 different glycan structures, including high mannose, complex and hybrid N-glycans, linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. Altogether, the N-glycan structures determined revealed that in donkey milk lactoferrin most of the N-glycans identified are neutral complex/hybrid. Actually, 10 neutral non-fucosylated complex/hybrid N-glycans and 4 neutral fucosylated complex/hybrid N-glycans were found. In addition, 2 high mannose N-glycans, 4 sialylated fucosylated complex/hybrid N-glycans and 6 sialylated non-fucosylatedN-glycans, one of which containing N-glycolylneuramin acid (Neu5Gc), were found. A comparison of the glycosylation profile of donkey milk lactoferrin with respect to that of human, bovine and goat milk lactoferrin is reported.

2016-08-25 | PXD004289 | Pride

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