scholarly journals Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus

2016 ◽  
Vol 7 ◽  
Author(s):  
Xiaoming Song ◽  
Jinpeng Wang ◽  
Xiao Ma ◽  
Yuxian Li ◽  
Tianyu Lei ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Evolutionary Trajectory ◽  
Expression Bias

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2020 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7,500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7,500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2020 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7,500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7,500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2020 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach.Results: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7,500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus.Conclusions: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7,500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

scholarly journals Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Jian Wu ◽  
Li Lin ◽  
Meiling Xu ◽  
Peipei Chen ◽  
Dongxiao Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Level ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

scholarly journals Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

2019 ◽  
Author(s):  
Kevin A. Bird ◽  
Chad Niederhuth ◽  
Shujun Ou ◽  
Malia Gehan ◽  
J. Chris Pires ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Gene Network ◽  
Phenotypic Diversity ◽  
Duplicate Genes ◽  
Network Analyses ◽  
Expression Bias ◽  
Plant Hybridization ◽  
Single Nucleus ◽  
Frequent Observation

AbstractInterspecific hybridization and allopolyploidization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is “dominant” over the other subgenome, having a greater number of reatined duplicate genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations. We found that the same subgenome was consistently more dominantly expressed in all lines and generations. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the Brassica oleracea derived ‘C’ subgenome in all lines and generations. These differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting subgenome dominance is related to inherited parental genome differences rather than a byproduct of allopolyploidization. Gene network analyses indicated an enrichment for network interactions and several biological functions for ‘C’ subgenome biased pairs, but no enrichment was observed for ‘A’ subgenome biased pairs. These findings demonstrate that “replaying the evolutionary tape” in allopolyploids results in repeatable and predictable subgenome expression dominance patterns based on preexisting genetic differences among the parental species. These findings have major implications regarding the genotypic and phenotypic diversity observed following plant hybridization in both ecological and agricultural contexts.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2019 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Expression Level ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background Allopolyploids were widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modification so as to show stronger growth vigor and adaptability. To explore the changes of homologous gene expression pattern in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after about 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using RNA sequencing approach. Results Results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after about 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were down-regulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both two comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo) and these pathways were all down-regulated in four tissues of B. napus. In addition, the homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis the expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additivity expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue, specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was true in leaves and flowers. More transgressive up-regulation expression gene pairs were found in B. napus. Conclusions In general, these results can provide a comprehensive understanding of the changes of homologous gene expression patterns in natural B. napus after about 7,500 years of evolution and domestication, and enhance our understanding of allopolyploids.

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