scholarly journals Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Libin Zhang ◽  
Jianjie He ◽  
Hongsheng He ◽  
Jiangsheng Wu ◽  
Maoteng Li
Keyword(s):  
Gene Expression ◽  
Brassica Oleracea ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Intergeneric Hybrids ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Distant Hybridization ◽  
Genome Wide ◽  
Expression Level Dominance

AbstractRaphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents.

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

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.

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 ◽  
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.

scholarly journals Alterations in global gene expression patterns resulting from 10 days of endurance training in humans

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Nigel Keith Stepto ◽  
Timothy John Burton ◽  
Therese Griersmith ◽  
David Powell ◽  
Benedict James Canny
Keyword(s):  
Gene Expression ◽  
Endurance Training ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Gene Expression Patterns

scholarly journals Global gene expression patterns in response to white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral

2019 ◽  
Author(s):  
Carly D. Kenkel ◽  
Veronique J.L. Mocellin ◽  
Line K. Bay
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Thermal Stress ◽  
Stress Response ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Host Protein ◽  
Gene Expression Patterns ◽  
White Patch

AbstractThe mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing symbiont loss from the abiotic stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in P. lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of abiotic stress from expression patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. The meta-analysis revealed that expression patterns in WPS-affected tissues were significantly correlated with prior studies examining short-term thermal stress responses. This correlation was independent of symbiotic state, as the strongest correlations were found between WPS adults and both symbiotic adult and aposymbiotic coral larvae experiencing thermal stress, suggesting that the majority of expression changes reflect a non-specific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration, and highlights unique responses to bleaching in an anemone model which engages in a non-obligate symbiosis.

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