Abstract
Rediploidization is considered to be a part of the evolutionary history of allotetraploids, and resulted in the emergence of novel epigenetic regulatory activities. To study the changing patterns of gene expression following the reduction of a genome by 50%, we used RNA-seq and quantitative real-time PCR (qPCR) to investigate total gene expression and homoeolog expression in three hybrids of a C. auratus red var. (2n = 100, ♀) (R) and C. carpio (2n = 100, ♂) (C) (i.e., F1, F18, and G4) and their original parents. A comparison of homoeolog expression between G4 and F18 identified 7 genes (0.22%) that exhibited novel R/C homoeolog expression patterns in G4, while 4 genes (0.12%) were affected by R/C homoeolog silencing. We determined the direction and extent of the homoeolog expression bias (HEB). The C-HEB genes (i.e., nrp1a and igf1) and R-HEB genes (i.e., fgf23 and esm1) provided insights into the effects of the dominance of one parental homoeolog expression on growth regulation. This dominance may contribute to the rapid growth of G4 fish. Our findings may be relevant for clarifying the relationship between growth heterosis and differences in homoeolog expression patterns.
Highlights
All teleosts underwent at least three rounds of whole-genome duplication (WGD) approximately 320 million years ago (Mya)
The changes in homoeolog expression levels caused by a rediplodization event were investigated by comparison of homoeolog-specific single nucleotide polymorphisms (SNPs) between the reference genomes of C. auratus red var. and C. carpio
To clarify the effects of rediploidization on transcript abundance, three hybrid lineages of the C. auratus red var. × C. carpio with different ploidy levels (i.e., F1, F18, and G4) and their original parents were analyzed[15,16] (Table 1 and Fig. 1)
Summary
All teleosts underwent at least three rounds of whole-genome duplication (WGD) (i.e., teleost-specific WGD) approximately 320 million years ago (Mya). Some studies have concluded that all WGD events were induced by hybridizations and led to polyploidizations, including emerge of allotetraploidizations origin from hybrid of C. auratus red var. The silencing of homoeologs (i.e., originating from a parental gene), gene loss, and the formation of novel genes have contributed to the development of new specie[7] These studies provided insights into the rediploidization process, which has not been fully characterized. The allotetraploid hybrid lineage (from 2n to 4n) and the diploid gynogenetic lineage (back to 2n from 4n) with two genome level changes provided an excellent experimental system for the investigation of genetic process regarding the allotetraploidization and rediploidization events. The changes in homoeolog expression levels caused by a rediplodization event were investigated by comparison of homoeolog-specific single nucleotide polymorphisms (SNPs) between the reference genomes of C. auratus red var. We compared the diploid gynogenetic fish with allodiploid and allotetraploid hybrids of the C. auratus red var. × C. carpio to investigate the changes in homoeolog expression levels induced by different rediploidization mechanisms
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