Abstract
BackgroundHybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is sparse for vertebrates.ResultsWe successfully obtained an F1 generation (including allodiploid hybrids and triploid hybrids) from female Megalobrama amblycephala Yih (BSB, 2n = 48) × male Xenocypri davidi Bleeker (YB, 2n = 48). The duplicated-gene expression patterns of the two types of hybrids were explored using RNA-Seq data. In total, 5.44 × 108 (69.32 GB) clean reads and 499,631 assembled unigenes were obtained from the testis transcriptomes. The sequence similarity analysis of 4265 orthologs revealed that the merged genomes were dominantly expressed in different ploidy hybrids. The differentially expressed genes in the two types of hybrids were asymmetric compared with those in both parents. Furthermore, the genome-wide expression level dominance (ELD) was biased toward the maternal BSB genome in both the allodiploid and triploid hybrids. In addition, the dosage-compensation mechanisms that reduced the triploid expression levels to the diploid state were determined in the triploid hybrids.ConclusionsOur results indicate that divergent genomes undergo strong interactions and domination in allopolyploid offspring. Genomic merger has a greater effect on the gene-expression patterns than genomic doubling. The various expression mechanisms (including maternal effect and dosage compensation) in different ploidy hybrids suggest that the initial genomic merger and doubling play important roles in polyploidy adaptation and evolution.
Highlights
Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation
Transcriptome assembly and annotation To examine the changes in the global transcriptomic profile, we obtained twelve testis transcriptomes from two parents, i.e., Megalobrama amblycephala Yih (BSB) and Xenocypri davidi Bleeker (YB), and their F1 hybrids,i.e., Allodiploid hybrid (2nBY) and Triploid hybrid (3nBY)
The transcripts from all twelve samples were clustered by CD-HIT, which yielded a total of 499,631(261.8 Mb) reference sequences, with an N50 of 634 bp
Summary
Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Hybridization and polyploidization are the driving forces of genomic evolution and speciation resulting from the instantaneous merger or doubling of two or more sets of divergent genomes [1, 2]. The reunion of two divergent genomes in a common nucleus during allopolyploid speciation can lead to immediate and profound genome modifications, such as sequence elimination [9,10,11,12,13], epigenetic diversity [14,15,16], activation of genes and retroelements [17], and homoeologous. Genetic and epigenetic changes are subject to selection and adaptation, and additional genes may be activated for allopolyploids to occupy an environmental niche [22]. Previous studies have documented that some important advantageous quality traits, such as vegetable and oil production [23], seed glucosinolate content [24], and cotton long fibers [25], resulted from subgenomes undergoing favorable selection during allopolyploid formation and domestication
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