Genome expression balance in a triploid trihybrid vertebrate

Kyle E. McElroy, Robert D. Denton, Joel Sharbrough, Laura Bankers, Maurine Neiman, H. Lisle Gibbs

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Polyploidy is increasingly recognized as a driver of biological diversity.Howandwhy polyploidization affects gene expression is critical to understanding the link between ploidy elevation and diversification. In polyploid plants,multiple studies have demonstrated that ploidy elevation can confer major but variable consequences for gene expression, ranging fromgene-by-gene alterations to entirely silenced genomes. By contrast, animal polyploids remain largely uncharacterized. Accordingly, howanimals respond to andmanage polyploidy events is not understood. Here, we address this important knowledge gap by analyzing transcriptomes from a triploid hybrid animal, a unisexualAmbystomasalamander, and three sexualAmbystoma species that represent all three parental genomes in the unisexual.We used a novel bioinformatics pipeline that includes competitively mapping triploid sequences to a reference set of orthologous genes in the sexual species to evaluate subgenome expression. Our comparisons of gene expression levels across the three parental genomes revealed that the unisexual triploid displays a pattern of genome balance,where72%of the genes analyzed were expressed equally among the subgenomes. This result is strikingly different from the genome imbalance typically observed in hybrid polyploid plants. Our analyses represent the first to address gene expression in a triploid hybrid animal and introduce a novel bioinformatic framework for analyzing transcriptomic data.

Original languageEnglish (US)
Pages (from-to)968-980
Number of pages13
JournalGenome biology and evolution
Volume9
Issue number4
DOIs
StatePublished - Apr 2017
Externally publishedYes

Bibliographical note

Funding Information:
We thank K. Greenwald and J. Bogart for help with procuring salamanders, and A. Hernandez, X. Bai, and A. Michel for early discussions about project design. Salamanders were held in captivity under Ohio State IACUC protocol 2012A00000039, and we thank M. Parsley and M. Saccucci for assistance with caring for captive animals. This work was supported by the Ohio State University. Transcriptome sequencing was conducted at the Roy J. Carver Biotechnology Center, University of Illinois using funds from the Ohio State University. This work was also supported by the National Science Foundation under Grant No. NSF-MCB 1122176 to L.B., K.E.M, M.N., J.S., the University of Iowa Graduate College to L.B. and K.E.M., the Evelyn Hart Watson Fellowship to K.E.M, J.S., and the National Center for Science Education to K.E.M.

Publisher Copyright:
© The Author(s) 2017.

Keywords

  • Gene expression
  • Genome dominance
  • Hybridization
  • Polyploidy
  • Reproductive mode
  • Salamander

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