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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.


Gene expression compensation of remainder chromosomes in aneuploides. (A) The number of expressed genes (FPKM > 0) along remainder chromosomes. (B,C) Cumulative frequency (B) and relative frequency (C) for expressed genes [log2(FPKM)] are calculated by dividing gene expression into 26 expression bins.
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Figure 7: Gene expression compensation of remainder chromosomes in aneuploides. (A) The number of expressed genes (FPKM > 0) along remainder chromosomes. (B,C) Cumulative frequency (B) and relative frequency (C) for expressed genes [log2(FPKM)] are calculated by dividing gene expression into 26 expression bins.

Mentions: We noted that, after taking out expressed genes (FPKM > 0) along variant C2, the number of expressed genes of remainder genome significantly increased with the reduction on C2 and the trend was much stronger in monosomics (Figure 7A). Different coverage of sequencing between “Oro” (7.0) and monosomics (10.4) potentially accounted for their gap for the fact that some rare transcripts need higher depth to be detected (Tarazona et al., 2011), however, it loosely explained the difference between monosomics and isomics (10.6). Alternatively, the elevated expressed genes in deficient types compensated for the insufficiency of gene expression along C2. Consistent with this notion was that the distributions of relative frequency (Figure 7B) and cumulative frequency (Figure 7C) of gene expressions (FPKM > 0) were statistically indistinguishable for the three types (Kolmogorov–Smirnov test, the P-value were always approximate 1). Although the average of gene expression of remainder genome was compensatory upregulation in both aneuploids (the fold change was 1.53 in monosomics and 1.16 in isomics), the downregulated genes were dominant (11,914 vs. 18,581 in Oro vs. mono, 19,720 vs. 18,504 in Oro vs. ; χ2 test, P < 0.01), suggesting a higher variable extents of upregulated genes. To determine the bias of up- or down-regulated genes, the genes of remainder genome were classified into the low (0 < FPKM < 10), medium (10 < FPKM < 100) or high (FPKM > 100) expression levels, in comparison with those of “Oro.” For the low expression level, the upregulated genes were significantly more than downregulated genes in both pairs (χ2 test, P < 0.01). For the medium and high levels, the skew changed to downregulated genes (χ2 test, P < 0.01), but the average gene expression within the two levels were still higher in both aneuploids. All together, these evidences suggested that a compensatory mechanism by upregulation of certain genes of remainder genome formed to respond to the C2 loss at RNA level in 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)

Gene expression compensation of remainder chromosomes in aneuploides. (A) The number of expressed genes (FPKM > 0) along remainder chromosomes. (B,C) Cumulative frequency (B) and relative frequency (C) for expressed genes [log2(FPKM)] are calculated by dividing gene expression into 26 expression bins.
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Related In: Results  -  Collection

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Figure 7: Gene expression compensation of remainder chromosomes in aneuploides. (A) The number of expressed genes (FPKM > 0) along remainder chromosomes. (B,C) Cumulative frequency (B) and relative frequency (C) for expressed genes [log2(FPKM)] are calculated by dividing gene expression into 26 expression bins.
Mentions: We noted that, after taking out expressed genes (FPKM > 0) along variant C2, the number of expressed genes of remainder genome significantly increased with the reduction on C2 and the trend was much stronger in monosomics (Figure 7A). Different coverage of sequencing between “Oro” (7.0) and monosomics (10.4) potentially accounted for their gap for the fact that some rare transcripts need higher depth to be detected (Tarazona et al., 2011), however, it loosely explained the difference between monosomics and isomics (10.6). Alternatively, the elevated expressed genes in deficient types compensated for the insufficiency of gene expression along C2. Consistent with this notion was that the distributions of relative frequency (Figure 7B) and cumulative frequency (Figure 7C) of gene expressions (FPKM > 0) were statistically indistinguishable for the three types (Kolmogorov–Smirnov test, the P-value were always approximate 1). Although the average of gene expression of remainder genome was compensatory upregulation in both aneuploids (the fold change was 1.53 in monosomics and 1.16 in isomics), the downregulated genes were dominant (11,914 vs. 18,581 in Oro vs. mono, 19,720 vs. 18,504 in Oro vs. ; χ2 test, P < 0.01), suggesting a higher variable extents of upregulated genes. To determine the bias of up- or down-regulated genes, the genes of remainder genome were classified into the low (0 < FPKM < 10), medium (10 < FPKM < 100) or high (FPKM > 100) expression levels, in comparison with those of “Oro.” For the low expression level, the upregulated genes were significantly more than downregulated genes in both pairs (χ2 test, P < 0.01). For the medium and high levels, the skew changed to downregulated genes (χ2 test, P < 0.01), but the average gene expression within the two levels were still higher in both aneuploids. All together, these evidences suggested that a compensatory mechanism by upregulation of certain genes of remainder genome formed to respond to the C2 loss at RNA level in 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.