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Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
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Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
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Journal Article
Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
2021
Overview
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.
Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 45
/ 631/601
/ Alternative Splicing - genetics
/ Animal Genetics and Genomics
/ Animals
/ Biomedical and Life Sciences
/ Carp
/ Diploids
/ Ecotypes
/ Genes
/ Genome
/ Genomes
/ Goldfish
/ Molecular Sequence Annotation
/ Proteins
/ Splicing
/ Survival
/ Synteny
