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

Zool Res. 2019 Jul 18;40(4):293-304. doi: 10.24272/j.issn.2095-8137.2019.042. Epub 2019 Jun 3.

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.

Keywords: Allele-specific alternative splicing; Allele-specific expression; Cis-regulatory elements; Hybrid species.

MeSH terms

  • Alleles*
  • Alternative Splicing*
  • Animals
  • Base Sequence
  • Cattle / genetics*
  • Equidae / genetics*
  • Gene Expression Regulation
  • Hybridization, Genetic / genetics*
  • RNA / genetics
  • RNA / metabolism

Substances

  • RNA

Associated data

  • GENBANK/PRJNA387435, PRJNA387436

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (31572381), National Thousand Youth Talents Plan of the International Science and Technology Cooperation Project of China (2013DFA31420), and Science and Technology Innovation Capability Promotion Program of the Science and Technology Department of Qinghai Province (2015-ZJ-712)