Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Li Ren,Jun Wang,Chun Zhang,Wuhui Li,Jie Chen,Chenchen Tang,Jun Xiao,Shaojun Liu,Yafeng Xiong,Yi Zhou,Jing Wang,Xingjun Tan,Min Tao,Jialin Cui

doi:10.1186/s12864-016-3424-5

Abstract

BackgroundPolyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates.ResultsWe generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring.ConclusionsOur results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation.

Highlights

Polyploidy and hybridization are both recognized as major forces in evolution
Transcriptome assembly To examine the changes in the global transcriptomic profile in triploid of Ctenopharyngodon idellus and Megalobrama amblycephala (GB), we obtained nine liver transcriptomes from maternal Ctenopharyngodon idellus (GC), paternal Megalobrama amblycephalae (BSB), and triploid offspring GB (Fig. 1)
The results showed that the number of homoeolog expression bias (HEB) genes was unbalanced in triploid with respect to the original parent was inclined to maternal GC genome (Fig. 4a)

Summary

Introduction

Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. Polyploid hybrids that play a role in the origin of plant and animal species have been studied for many years. Hybridization is viewed as a destructive process that counteracts speciation and delays evolution [1]. Polyploidy and hybridization can be viewed separately, the processes often occur together in the form of allopolyploidy [3]. The molecular mechanisms of gene expression regulation in allotetraploids are well studied in plants. Only a few animal species, mostly insects and fish, have been recognized as being the result of hybridization and polyploidy [9]. Little has been done to understand the effects of ploidy increases on gene

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