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Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
- Source :
- Nature Genetics
- Publication Year :
- 2021
- Publisher :
- Springer Science and Business Media LLC, 2021.
-
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.<br />Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes.
- Subjects :
- Candidate gene
Carps
Karyotype
Sequence assembly
Biology
Synteny
Article
Evolution, Molecular
Common carp
Negative selection
Species Specificity
Goldfish
Genetics
Animals
Selection, Genetic
Phylogeny
Likelihood Functions
Genome
Dosage compensation
Base Sequence
Genetic Variation
food and beverages
Molecular Sequence Annotation
Genomics
Genome project
Tetraploidy
Alternative Splicing
Gene Expression Regulation
Evolutionary biology
Gene expression
Ploidy
Zoology
Subjects
Details
- ISSN :
- 15461718 and 10614036
- Volume :
- 53
- Database :
- OpenAIRE
- Journal :
- Nature Genetics
- Accession number :
- edsair.doi.dedup.....2db882d7cfb06b87fdaaca66e58d05fd