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Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L.

Zhu B, Shao Y, Pan Q, Ge X, Li Z - Front Plant Sci (2015)

Bottom Line: In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome.But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss.These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

View Article: PubMed Central - PubMed

Affiliation: National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China.

ABSTRACT
Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the isomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than isomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

No MeSH data available.


GO assignment of annotated DEGs in “Oro vs. mono” and “Oro vs. .” DEGs are annotated by three categories: cellular component, molecular functions, and biological process. The left and right of x-axis represent the up-regulated (Red for “Oro vs. mono” and blue for “Oro vs. ”) and down-regulated genes (Green for “Oro vs. mono” and cyan for “Oro vs. ”).
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Figure 6: GO assignment of annotated DEGs in “Oro vs. mono” and “Oro vs. .” DEGs are annotated by three categories: cellular component, molecular functions, and biological process. The left and right of x-axis represent the up-regulated (Red for “Oro vs. mono” and blue for “Oro vs. ”) and down-regulated genes (Green for “Oro vs. mono” and cyan for “Oro vs. ”).

Mentions: Among these GO terms, “cell” and “cell part,” “catalytic activity” and “binding,” “metabolic process” and “cellular process” invariably occupied the majority for both paired comparisons, in “cellular component,” “molecular function” and “biological process,” respectively. And several terms merely contained sparse genes for both pairs, such as “protein tag” in “cellular component” and “cell killing” in “molecular function” (Figure 6). It was noteworthy that the term of “structural molecule activity” was significantly overrepresented by the up-regulated genes for both pairs (χ2 test, P < 0.01), which probably supported the view that the structure of genome was undergoing a period of instability in aneuploidy (Huettel et al., 2008; Zhu et al., 2012). Another finding for both pairs was that the downregulated genes was dominant in the term of “transcription regulator activity” (χ2 test, P < 0.01), consistent with the fact of a priority of downregulated gene expression. However, in term of “translation regulator activity,” the upregulated genes manifested booming (χ2 test, P < 0.01), strengthening the idea that some transcript expression profilings would be adjusted at the process of translation (Stingele et al., 2012). It seemed likely that the sophisticated mechanisms responding to deficiency of C2 not only functioned at the beginning of transcription but also threaded throughout the process of gene expression. Subsequently, the GO annotation of common DEGs was performed to manifest the divergence of gene expression between transcription and translation again. We noticed that despite immense gulf of DEGs number between two pairs, the proportions of DEGs of GO terms were exceedingly similar for both pairs (Correlation test, R = 0.9997), considering a comparatively high proportion of common DEGs and an extremely similar variation tendency of fold change of each chromosome, which further highlighted the speculation that a similar mechanism emerged to respond to the missing of C2 for both aneuploids.


Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L.

Zhu B, Shao Y, Pan Q, Ge X, Li Z - Front Plant Sci (2015)

GO assignment of annotated DEGs in “Oro vs. mono” and “Oro vs. .” DEGs are annotated by three categories: cellular component, molecular functions, and biological process. The left and right of x-axis represent the up-regulated (Red for “Oro vs. mono” and blue for “Oro vs. ”) and down-regulated genes (Green for “Oro vs. mono” and cyan for “Oro vs. ”).
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Related In: Results  -  Collection

License
Show All Figures
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Figure 6: GO assignment of annotated DEGs in “Oro vs. mono” and “Oro vs. .” DEGs are annotated by three categories: cellular component, molecular functions, and biological process. The left and right of x-axis represent the up-regulated (Red for “Oro vs. mono” and blue for “Oro vs. ”) and down-regulated genes (Green for “Oro vs. mono” and cyan for “Oro vs. ”).
Mentions: Among these GO terms, “cell” and “cell part,” “catalytic activity” and “binding,” “metabolic process” and “cellular process” invariably occupied the majority for both paired comparisons, in “cellular component,” “molecular function” and “biological process,” respectively. And several terms merely contained sparse genes for both pairs, such as “protein tag” in “cellular component” and “cell killing” in “molecular function” (Figure 6). It was noteworthy that the term of “structural molecule activity” was significantly overrepresented by the up-regulated genes for both pairs (χ2 test, P < 0.01), which probably supported the view that the structure of genome was undergoing a period of instability in aneuploidy (Huettel et al., 2008; Zhu et al., 2012). Another finding for both pairs was that the downregulated genes was dominant in the term of “transcription regulator activity” (χ2 test, P < 0.01), consistent with the fact of a priority of downregulated gene expression. However, in term of “translation regulator activity,” the upregulated genes manifested booming (χ2 test, P < 0.01), strengthening the idea that some transcript expression profilings would be adjusted at the process of translation (Stingele et al., 2012). It seemed likely that the sophisticated mechanisms responding to deficiency of C2 not only functioned at the beginning of transcription but also threaded throughout the process of gene expression. Subsequently, the GO annotation of common DEGs was performed to manifest the divergence of gene expression between transcription and translation again. We noticed that despite immense gulf of DEGs number between two pairs, the proportions of DEGs of GO terms were exceedingly similar for both pairs (Correlation test, R = 0.9997), considering a comparatively high proportion of common DEGs and an extremely similar variation tendency of fold change of each chromosome, which further highlighted the speculation that a similar mechanism emerged to respond to the missing of C2 for both aneuploids.

Bottom Line: In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome.But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss.These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

View Article: PubMed Central - PubMed

Affiliation: National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China.

ABSTRACT
Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the isomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than isomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

No MeSH data available.