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

BMC Genomics

Research Article

Wuhui Li¹  Jing Wang¹  Jun Wang¹  Chun Zhang¹  Chenchen Tang¹  Xingjun Tan¹  Jun Xiao¹  Yafeng Xiong¹  Jie Chen¹  Li Ren¹  Jialin Cui¹  Min Tao¹  Shaojun Liu¹  Yi Zhou¹ 

[1] State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, 410081, Changsha, China;

关键词: Dosage compensation;    Genomic dominance;    Biased expression;    Triploid;    Transcriptome;   

DOI  :  10.1186/s12864-016-3424-5

 received in 2015-08-13, accepted in 2016-12-14,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017