Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids

• Main Authors: Yu Wang, Shan Gao, Yue Zhao, Wei-Huang Chen, Jun-Jie Shao, Ni-Ni Wang, Ming Li, Guang-Xian Zhou, Lei Wang, Wen-Jing Shen, Jing-Tao Xu, Wei-Dong Deng, Wen Wang, Yu-Lin Chen, Yu Jiang
• Format: Article
• Language: English
• Published: Science Press, PR China 2019-07-01
• Series: Zoological Research
• Subjects: Allele-specific alternative splicing; Allele-specific expression; Cis-regulatory elements; Hybrid species
• Online Access: http://www.zoores.ac.cn/EN/abstract/abstract3955.shtml
• ISSN: 2095-8137; 2095-8137

Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%–8.7% and 10.8%–16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.