Comparative Transcriptomics Uncover the Uniqueness of Oocyte Development in the Donkey

Abstract

The donkey is an important domestic animal, however the number of donkeys world-wide is currently declining. It is therefore important to protect their genetic resources and to elaborate the regulatory mechanisms of donkey reproduction, particularly, oocyte development. Here, we adopted comparative transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) to uncover the uniqueness of donkey oocyte development compared to cattle, sheep, pigs, and mice, during the period from germinal vesicle (GV) to metaphase II (MII). Significantly, we selected 36 hub genes related to donkey oocyte development, including wee1-like protein kinase 2 (WEE2). Gene Ontology (GO) analysis suggested that these genes are involved in the negative regulation of cell development. Interestingly, we found that donkey specific differentially expressed genes (DEGs) were involved in RNA metabolism and apoptosis. Moreover, the results of WGCNA showed species-specific gene expression patterns. We conclude that, compared to other species, donkey oocytes express a large number of genes related to RNA metabolism to maintain normal oocyte development during the period from GV to MII.

Identification of unique transcriptomic signatures through integrated multispecies comparative analysis and WGCNA in bovine oocyte development

“…Differential expression analysis suggested that most genes were down-regulated as oocytes progressed, which was consistent with previous studies [ 17 ], as the transcriptional activity of mammalian oocytes was silenced during the GV period before the meiotic restart [ 18 , 19 ]. After transcriptional silencing, the oocyte genome undergoes the first and second meiosis, and the transcriptional activity is not restored until cleavage of the early embryo after fertilisation [ 20 ].…”

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

“…Consequently, Tian et al [101] performed an integrated analysis of mRNA and miRNA in the testis and cauda epididymidis and found some key genes (Table 4) and pathways (focal adhesion, ECM-receptor interaction, actin cytoskeleton regulation, rap1 signaling pathway, and PI3K-Akt signaling pathway) that are possibly involved in the regulation of sperm maturation and motility [101]. Next-generation RNA sequencing (RNA-seq) technology was used to compare the gene expression profiles of donkey and horse oocytes during the early stages of development [102]. The researchers found that several genes related to oocyte development, chromatin remodeling, and cell cycle regulation were differentially expressed in donkey oocytes compared to horse oocytes [102], as shown in Table 4.…”

Multispecies comparative analysis reveals transcriptional specificity during Mongolian horse testicular development

“…During the development of RNA‐seq technology, to deal with the increasingly high‐throughput of biological sequencing data, a large number of protocols have been developed. A growing number of studies show that weighted gene co‐expression network analysis (WGCNA) is good for building gene networks, and can determine hub genes in the network (Langfelder & Horvath, 2008; Zhang, Zhang et al, 2022). Previous reports demonstrate the use of WGCNA to identify hub genes involved in regulating donkey oocyte development, and it has also been used to identify key genes regulating hepatocellular carcinoma progression (Yin et al, 2018; Zhang, Zhang, et al, 2022).…”

“…A growing number of studies show that weighted gene co‐expression network analysis (WGCNA) is good for building gene networks, and can determine hub genes in the network (Langfelder & Horvath, 2008; Zhang, Zhang et al, 2022). Previous reports demonstrate the use of WGCNA to identify hub genes involved in regulating donkey oocyte development, and it has also been used to identify key genes regulating hepatocellular carcinoma progression (Yin et al, 2018; Zhang, Zhang, et al, 2022). As yet, the in‐depth knowledge of Mongolian horse transcriptional profiles has not been studied.…”