title: De Novo Assembly of the Donkey White Blood Cell Transcriptome and a Comparative Analysis of Phenotype-Associated Genes between Donkeys and Horses.
abstract: Prior to the mechanization of agriculture and labor-intensive tasks, humans used donkeys (Equus africanus asinus) for farm work and packing. However, as mechanization increased, donkeys have been increasingly raised for meat, milk, and fur in China. To maintain the development of the donkey industry, breeding programs should focus on traits related to these new uses. Compared to conventional marker-assisted breeding plans, genome- and transcriptome-based selection methods are more efficient and effective. To analyze the coding genes of the donkey genome, we assembled the transcriptome of donkey white blood cells de novo. Using transcriptomic deep-sequencing data, we identified 264,714 distinct donkey unigenes and predicted 38,949 protein fragments. We annotated the donkey unigenes by BLAST searches against the non-redundant (NR) protein database. We also compared the donkey protein sequences with those of the horse (E. caballus) and wild horse (E. przewalskii), and linked the donkey protein fragments with mammalian phenotypes. As the outer ear size of donkeys and horses are obviously different, we compared the outer ear size-associated proteins in donkeys and horses. We identified three ear size-associated proteins, HIC1, PRKRA, and KMT2A, with sequence differences among the donkey, horse, and wild horse loci. Since the donkey genome sequence has not been released, the de novo assembled donkey transcriptome is helpful for preliminary investigations of donkey cultivars and for genetic improvement.
authors.affiliation: Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Feng-Yun
authors.initials: FY
authors.lastname: Xie
authors.affiliation: College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Black Donkey Research Institute, Shandong Dongeejiao Company Limited, Liaocheng, Shandong, 252000, China.
authors.forename: Yu-Long
authors.initials: YL
authors.lastname: Feng
authors.affiliation: Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Hong-Hui
authors.initials: HH
authors.lastname: Wang
authors.affiliation: College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Black Donkey Research Institute, Shandong Dongeejiao Company Limited, Liaocheng, Shandong, 252000, China.
authors.forename: Yun-Feng
authors.initials: YF
authors.lastname: Ma
authors.affiliation: College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Black Donkey Research Institute, Shandong Dongeejiao Company Limited, Liaocheng, Shandong, 252000, China.
authors.forename: Yin-Chao
authors.initials: YC
authors.lastname: Wang
authors.affiliation: Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Shen
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Qing-Jie
authors.initials: QJ
authors.lastname: Pan
authors.affiliation: Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Shen
authors.initials: S
authors.lastname: Yin
authors.affiliation: College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Yu-Jiang
authors.initials: YJ
authors.lastname: Sun
authors.affiliation: Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
authors.forename: Jun-Yu
authors.initials: JY
authors.lastname: Ma
mesh_terms: D000818:Animals; D030562:Databases, Protein; D018397:Equidae / Q000235:genetics* / Q000378:metabolism; D006736:Horses / Q000235:genetics* / Q000378:metabolism; D007962:Leukocytes / Q000378:metabolism*; D010641:Phenotype; D059467:Transcriptome