Correlated expression of retrocopies and parental genes in zebrafish

Mol Genet Genomics. 2016 Apr;291(2):723-37. doi: 10.1007/s00438-015-1140-5. Epub 2015 Nov 11.


Previous studies of the function and evolution of retrocopies in plants, Drosophila and non-mammalian chordates provided new insights into the origin of novel genes. However, little is known about retrocopies and their parental genes in teleosts, and it remains obscure whether there is any correlation between them. The present study aimed to characterize the spatial and temporal expression profiles of retrogenes and their parental genes based on RNA-Seq data from Danio rerio embryos and tissues from adult. Using a modified pipeline, 306 retrocopies were identified in the zebrafish genome, most of which exhibited ancient retroposition, and 76 of these showed a Ks < 2.0. Expression of a retrocopy is generally expected to present no correlation with its parental gene, as regulatory regions are not part of the retroposition event. Here, this assumption was tested based on RNA-Seq data from eight stages and thirteen tissue types of zebrafish. However, the result suggested that retrocopies displayed correlated expression with their parental genes. The level of correlation was found to decrease during embryogenesis, but to increase slightly within a tissue using Ks as the proxy for the divergence time. Tissue specificity was also observed: retrocopies were found to be expressed at a more specific level compared with their parental genes. Unlike Drosophila, which has sex chromosomes, zebrafish do not show testis-biased expression. Our study elaborated temporal and spatial patterns of expression of retrocopies in zebrafish, examined the correlation between retrocopies and parental genes and analyzed potential source of regulated elements of retrocopies, which lay a foundation for further functional study of retrocopies.

Keywords: Expression pattern; Retroposition; Specificity; Transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Evolution, Molecular*
  • Gene Duplication
  • Gene Expression Regulation, Developmental
  • Genome
  • High-Throughput Nucleotide Sequencing / methods*
  • RNA / biosynthesis
  • RNA / genetics*
  • Retroelements / genetics
  • Tissue Distribution / genetics
  • Transcriptome / genetics
  • Zebrafish / genetics*
  • Zebrafish / growth & development


  • Retroelements
  • RNA