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Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains.

Yang M, Ohnuki S, Ohya Y - BMC Genomics (2014)

Bottom Line: However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model.Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg, FSB-101, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Chiba Prefecture, Japan. ohya@k.u-tokyo.ac.jp.

ABSTRACT

Background: Phenotypes are variable within species, with high phenotypic variation in the fitness and cell morphology of natural yeast strains due to genetic variation. A gene deletion collection of yeast laboratory strains also contains phenotypic variations, demonstrating the involvement of each gene and its specific function. However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.

Results: The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model. The gene deletion strains had higher morphological variance than the natural strains. Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

Conclusion: Based on the morphological analysis, we discovered gene deletion mutants whose morphologies were not seen in nature. Our multivariate approach to the morphological diversity provided a new insight into the evolution and species conservation of yeast.

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Annotations of the genes deleted in the heteroclite 36 homozygous mutants. (A) Hierarchical cluster analysis of the 13 GOs. The dendrogram was constructed with complete linkage with the distances of GOs. The colored GOs indicate the representative four GOs in Figure 7B. The asterisks denote the GOs with significant differences between the annotated genes and the natural strains with PC scores at P <0.05 after Bonferroni correction by MANOVA. (B) Distribution of PC scores. Blue, orange, and black circles indicate the natural strains, the gene deletion strains, and BY4743, respectively. Red, magenta, cyan, and green circles denote the gene deletion strains with genes annotated to the GO terms of “cellular response to heat” (GO:0034605), “polysome” (GO:00005844), “recombinational repair” (GO:0000725), and “protein acylation” (GO:0043543), respectively. Gray dashed lines indicate the percentile of P =0.05 after Bonferroni correction to detect the heteroclite strains by one-sample two-sided tests of normal distribution.
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Fig7: Annotations of the genes deleted in the heteroclite 36 homozygous mutants. (A) Hierarchical cluster analysis of the 13 GOs. The dendrogram was constructed with complete linkage with the distances of GOs. The colored GOs indicate the representative four GOs in Figure 7B. The asterisks denote the GOs with significant differences between the annotated genes and the natural strains with PC scores at P <0.05 after Bonferroni correction by MANOVA. (B) Distribution of PC scores. Blue, orange, and black circles indicate the natural strains, the gene deletion strains, and BY4743, respectively. Red, magenta, cyan, and green circles denote the gene deletion strains with genes annotated to the GO terms of “cellular response to heat” (GO:0034605), “polysome” (GO:00005844), “recombinational repair” (GO:0000725), and “protein acylation” (GO:0043543), respectively. Gray dashed lines indicate the percentile of P =0.05 after Bonferroni correction to detect the heteroclite strains by one-sample two-sided tests of normal distribution.

Mentions: Summary of the phenotypes annotated to the 36 heteroclite genes. Annotations of the phenotypes in Additional file 10: Table S3 are summarized. Asterisks indicate the genes annotated to the GOs as detected by MANOVA (Figure 7A and Additional file 12: Table S4).


Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains.

Yang M, Ohnuki S, Ohya Y - BMC Genomics (2014)

Annotations of the genes deleted in the heteroclite 36 homozygous mutants. (A) Hierarchical cluster analysis of the 13 GOs. The dendrogram was constructed with complete linkage with the distances of GOs. The colored GOs indicate the representative four GOs in Figure 7B. The asterisks denote the GOs with significant differences between the annotated genes and the natural strains with PC scores at P <0.05 after Bonferroni correction by MANOVA. (B) Distribution of PC scores. Blue, orange, and black circles indicate the natural strains, the gene deletion strains, and BY4743, respectively. Red, magenta, cyan, and green circles denote the gene deletion strains with genes annotated to the GO terms of “cellular response to heat” (GO:0034605), “polysome” (GO:00005844), “recombinational repair” (GO:0000725), and “protein acylation” (GO:0043543), respectively. Gray dashed lines indicate the percentile of P =0.05 after Bonferroni correction to detect the heteroclite strains by one-sample two-sided tests of normal distribution.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4221665&req=5

Fig7: Annotations of the genes deleted in the heteroclite 36 homozygous mutants. (A) Hierarchical cluster analysis of the 13 GOs. The dendrogram was constructed with complete linkage with the distances of GOs. The colored GOs indicate the representative four GOs in Figure 7B. The asterisks denote the GOs with significant differences between the annotated genes and the natural strains with PC scores at P <0.05 after Bonferroni correction by MANOVA. (B) Distribution of PC scores. Blue, orange, and black circles indicate the natural strains, the gene deletion strains, and BY4743, respectively. Red, magenta, cyan, and green circles denote the gene deletion strains with genes annotated to the GO terms of “cellular response to heat” (GO:0034605), “polysome” (GO:00005844), “recombinational repair” (GO:0000725), and “protein acylation” (GO:0043543), respectively. Gray dashed lines indicate the percentile of P =0.05 after Bonferroni correction to detect the heteroclite strains by one-sample two-sided tests of normal distribution.
Mentions: Summary of the phenotypes annotated to the 36 heteroclite genes. Annotations of the phenotypes in Additional file 10: Table S3 are summarized. Asterisks indicate the genes annotated to the GOs as detected by MANOVA (Figure 7A and Additional file 12: Table S4).

Bottom Line: However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model.Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg, FSB-101, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Chiba Prefecture, Japan. ohya@k.u-tokyo.ac.jp.

ABSTRACT

Background: Phenotypes are variable within species, with high phenotypic variation in the fitness and cell morphology of natural yeast strains due to genetic variation. A gene deletion collection of yeast laboratory strains also contains phenotypic variations, demonstrating the involvement of each gene and its specific function. However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.

Results: The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model. The gene deletion strains had higher morphological variance than the natural strains. Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

Conclusion: Based on the morphological analysis, we discovered gene deletion mutants whose morphologies were not seen in nature. Our multivariate approach to the morphological diversity provided a new insight into the evolution and species conservation of yeast.

Show MeSH