Abstract
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.
Highlights
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies
We describe the genomes of P. tetrazona (2n: 50, Barbinae subfamily, Cyprinidae family, Cyprinoidei suborder) and P. guichenoti (2n: 50, Sarcocheilichthyinae subfamily, Gobionidae family, Cyprinoidei suborder), a high-quality common carp genome and an improved annotation of the goldfish genome
The contig N50 size was 1.42 Mb and almost 85.9% of all bases were anchored into 25 pseudo-chromosomes with an average length of 25.08 Mb (Supplementary Fig. 5)
Summary
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. The divergent structure evolution mechanisms underlying subgenome adaptation in polyploids include decreased sequence identity[6], relaxed purifying selection[7], transposon expansion[8], gene fractionation[7] and loss of genes and/or conserved genomic elements[6]. Both common carp (Cyprinus carpio) and goldfish (Carassius auratus) in the Cyprininae superfamily, Cyprinidae family, Cyprinoidei suborder are allo-tetraploid (2n: 100). We describe the genomes of P. tetrazona (2n: 50, Barbinae subfamily, Cyprinidae family, Cyprinoidei suborder) and P. guichenoti (2n: 50, Sarcocheilichthyinae subfamily, Gobionidae family, Cyprinoidei suborder), a high-quality common carp genome and an improved annotation of the goldfish genome. Resequencing 93 individuals uncovered the geographical genome architecture and domestication of common carp
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