Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids
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Yu Wang,
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Shan Gao,
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Yue Zhao,
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Chen Wei-Huang,
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Jun-Jie Shao,
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Wang Ni-Ni,
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Ming Li,
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Guang-Xian Zhou,
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Lei Wang,
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Wen-Jing Shen,
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Jing-Tao Xu,
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Wei-Dong Deng,
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Wen Wang,
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Yu-Lin Chen,
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Yu Jiang
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Abstract
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.
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