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However, the current insights into reproduction of donkeys are far from enough. To obtain a deeper understanding, the differential expression analysis and weighted gene co-expression network analysis (WGCNA) of transcriptomic data of testicular and epididymis tissues in donkeys were performed. In the result, there were 4313 differentially expressed genes (DEGs) in the two tissues, including 2047 enriched in testicular tissue and 2266 in epididymis tissue. WGCNA identified 1081 hub genes associated with testis development and 6110 genes with epididymal development. Next, the tissue-specific genes were identified with the above two methods, and the gene ontology (GO) analysis revealed that the epididymal-specific genes were associated with gonad development. On the other hand, the testis-specific genes were involved in the formation of sperm flagella, meiosis period, ciliary assembly, ciliary movement, etc. In addition, we found that eca-Mir-711 and eca-Mir-143 likely participated in regulating the development of epididymal tissue. Meanwhile, eca-Mir-429, eca-Mir-761, eca-Mir-200a, eca-Mir-191 and eca-Mir-200b potentially played an important role in regulating the development of testicular tissue. In short, these results will contribute to functional studies of the male reproductive trait in donkeys.<\/jats:p>","DOI":"10.3390\/genes13122339","type":"journal-article","created":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T03:02:37Z","timestamp":1670814157000},"page":"2339","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Transcriptional Specificity Analysis of Testis and Epididymis Tissues in Donkey"],"prefix":"10.3390","volume":"13","author":[{"given":"Mubin","family":"Yu","sequence":"first","affiliation":[{"name":"College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiamao","family":"Yan","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhua","family":"Guo","sequence":"additional","affiliation":[{"name":"Jiaozhou Agricultural and Rural Bureau, Jiaozhou 266300, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1193-2183","authenticated-orcid":false,"given":"Fali","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kexin","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuqin","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujiang","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Shen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7145-5702","authenticated-orcid":false,"given":"Junjie","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"51","DOI":"10.24272\/j.issn.2095-8137.2020.007","article-title":"Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences","volume":"41","author":"Ma","year":"2020","journal-title":"Zool. 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