Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish

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 t...

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Published inNature genetics Vol. 53; no. 10; pp. 1493 - 1503
Main Authors Li, Jiong-Tang, Wang, Qi, Huang Yang, Mei-Di, Li, Qing-Song, Cui, Ming-Shu, Dong, Zai-Jie, Wang, Hong-Wei, Yu, Ju-Hua, Zhao, Yu-Jie, Yang, Chen-Ru, Wang, Ya-Xin, Sun, Xiao-Qing, Zhang, Yan, Zhao, Ran, Jia, Zhi-Ying, Wang, Xi-Yin
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.10.2021
Nature Publishing Group
Subjects
38
45
631/208/199
631/208/212
631/601
Agriculture
Allopolyploid
Alternative Splicing - genetics
Animal Genetics and Genomics
Animals
Annotations
Base Sequence
Biomedical and Life Sciences
Biomedicine
Cancer Research
Carassius auratus
Carp
Carps - genetics
Chromosomes
Coexistence
Compensation
Cyprinus carpio
Diploids
Divergence
Divergent evolution
Dosage compensation
Ecotypes
Evolution
Evolution, Molecular
Gene Expression Regulation
Gene Function
Genes
Genetic aspects
Genetic research
Genetic Variation
Genome
Genomes
Goldfish
Goldfish - genetics
Homogeneity
Human Genetics
Karyotype
Likelihood Functions
Molecular Sequence Annotation
Natural history
Phylogenetics
Phylogeny
Proteins
Selection, Genetic
Species Specificity
Splicing
Structure
Survival
Synteny
Synteny - genetics
Tetraploidy
Zebrafish
China
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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. Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes.
AbstractList 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.
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.
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.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.
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.
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.
Audience Academic
Author Dong, Zai-Jie
Zhao, Ran
Jia, Zhi-Ying
Cui, Ming-Shu
Wang, Ya-Xin
Wang, Hong-Wei
Li, Jiong-Tang
Li, Qing-Song
Yu, Ju-Hua
Wang, Qi
Zhao, Yu-Jie
Wang, Xi-Yin
Sun, Xiao-Qing
Zhang, Yan
Huang Yang, Mei-Di
Yang, Chen-Ru
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  organization: North China University of Science and Technology
BackLink https://www.ncbi.nlm.nih.gov/pubmed/34594040$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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2021. The Author(s).
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Snippet How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the...
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SubjectTerms 38
45
631/208/199
631/208/212
631/601
Agriculture
Allopolyploid
Alternative Splicing - genetics
Animal Genetics and Genomics
Animals
Annotations
Base Sequence
Biomedical and Life Sciences
Biomedicine
Cancer Research
Carassius auratus
Carp
Carps - genetics
Chromosomes
Coexistence
Compensation
Cyprinus carpio
Diploids
Divergence
Divergent evolution
Dosage compensation
Ecotypes
Evolution
Evolution, Molecular
Gene Expression Regulation
Gene Function
Genes
Genetic aspects
Genetic research
Genetic Variation
Genome
Genomes
Goldfish
Goldfish - genetics
Homogeneity
Human Genetics
Karyotype
Likelihood Functions
Molecular Sequence Annotation
Natural history
Phylogenetics
Phylogeny
Proteins
Selection, Genetic
Species Specificity
Splicing
Structure
Survival
Synteny
Synteny - genetics
Tetraploidy
Zebrafish
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Title Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
URI https://link.springer.com/article/10.1038/s41588-021-00933-9
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Volume 53
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