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

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

10.21203/rs.2.11844/v5 ◽

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.

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

10.21203/rs.2.11844/v4 ◽

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

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

10.21203/rs.2.11844/v6 ◽

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.

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

10.21203/rs.2.11844/v2 ◽

2019 ◽

Author(s):

Mengdi Li ◽

Ruihua Wang ◽

Xiaoming Wu ◽

Jianbo Wang

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Expression Level ◽

Gene Expression Patterns ◽

Homologous Gene ◽

Gene Pairs ◽

Expression Bias ◽

Comparison Groups ◽

Homoeolog Expression Bias ◽

Expression Level Dominance

Abstract Background:Allopolyploids are widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger growth vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploidBrassica napus(AnAnCnCn) relative to its two diploid progenitors, B. rapa(ArAr) and B. oleracea(CoCo), after approximately7,500 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. napusafter approximately7,500 years of natural domestication, andmost differentially expressed genes (DEGs) in B. napuswere 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 (AnAnCnCnvs ArArand AnAnCnCnvs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, the homoeolog expression bias and expression level dominance (ELD) inB. napuswere thoroughly studied through analysis of the expression levels of 27609 B. rapa-B. oleraceaorthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napusmaintained 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 observed in leaves and flowers. More transgressive upregulationexpression, rather than downregulationexpression,was observedin 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. napusafter approximately 7,500 years of evolution and domestication and mayenhance our understanding of allopolyploids.

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

10.21203/rs.2.11844/v3 ◽

2020 ◽

Author(s):

Mengdi Li ◽

Ruihua Wang ◽

Xiaoming Wu ◽

Jianbo Wang

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Expression Level ◽

Gene Expression Patterns ◽

Homologous Gene ◽

Gene Pairs ◽

Expression Bias ◽

Comparison Groups ◽

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 allotetraploidBrassica 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. napusafter approximately 7,500 years of natural domestication, andmost differentially expressed genes (DEGs) in B. napuswere 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 (AnAnCnCnvs ArArand AnAnCnCnvs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, the homoeolog expression bias and expression level dominance (ELD) in B. napuswere thoroughly studied through analysis of the expression levels of 27609 B. rapa-B. oleraceaorthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napusmaintained 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 inB. 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 upregulationexpression, rather than downregulationexpression, was observedin 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. napusafter approximately 7,500 years of evolution and domestication and may enhance our understanding ofallopolyploidy.

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

BMC Genomics ◽

10.1186/s12864-018-4966-5 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 20

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

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

BMC Genomics ◽

10.1186/s12864-020-6747-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Mengdi Li ◽

Ruihua Wang ◽

Xiaoming Wu ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Expression Level ◽

Expression Bias ◽

Homoeolog Expression Bias ◽

Expression Level Dominance

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Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽

10.1186/s12864-021-07545-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jorge A. Ramírez-Tejero ◽

Jaime Jiménez-Ruiz ◽

Alicia Serrano ◽

Angjelina Belaj ◽

Lorenzo León ◽

...

Keyword(s):

Gene Expression ◽

Expression Pattern ◽

Growth And Development ◽

Expression Patterns ◽

Gene Expression Pattern ◽

Expression Level ◽

Resistant Cultivars ◽

Pathogen Invasion ◽

Wide Range ◽

Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

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