Asymmetric epigenetic modifications and homoeolog expression bias in the establishment and evolution of allopolyploid Brassica napus

2021 ◽  
Author(s):  
Mengdi Li ◽  
Weiqi Sun ◽  
Fan Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Epigenetic Modifications ◽  
Expression Bias ◽  
Homoeolog 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 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.

scholarly journals Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Tatsuhiro Nomaguchi ◽  
Yoshiaki Maeda ◽  
Tomoko Yoshino ◽  
Toru Asahi ◽  
Leila Tirichine ◽  
...  
Keyword(s):  
Marine Diatom ◽  
Expression Bias ◽  
Homoeolog Expression Bias

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 Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins

2021 ◽  
Vol 12 ◽  
Author(s):  
J. Lucas Boatwright ◽  
Cheng-Ting Yeh ◽  
Heng-Cheng Hu ◽  
Alfonso Susanna ◽  
Douglas E. Soltis ◽  
...  
Keyword(s):  
Gene Dosage ◽  
Expression Patterns ◽  
Genetic Material ◽  
Flowering Plant ◽  
Evolutionary Time ◽  
Specific Expression ◽  
Naturally Occurring ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Compare And Contrast

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.

Sign in / Sign up

Export Citation Format

Share Document