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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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Distribution of the number of genetic interactions. (A) Alignment of the gene deletion strains according to the number of genetic interactions. Red and orange crosses indicate the detected strains and the undetected strains, respectively. The number of genetic interactions of 77 strains was counted, as the remainder was not available [17]. (B) Boxplot of the number of genetic interactions. Grey, red and orange boxes indicate number of genetic interactions in 100 genes randomly selected from nonessential genes as a reference, heteroclite strains and remaining strains, respectively. Gene number available for genetic interaction data is shown in parentheses.
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Fig6: Distribution of the number of genetic interactions. (A) Alignment of the gene deletion strains according to the number of genetic interactions. Red and orange crosses indicate the detected strains and the undetected strains, respectively. The number of genetic interactions of 77 strains was counted, as the remainder was not available [17]. (B) Boxplot of the number of genetic interactions. Grey, red and orange boxes indicate number of genetic interactions in 100 genes randomly selected from nonessential genes as a reference, heteroclite strains and remaining strains, respectively. Gene number available for genetic interaction data is shown in parentheses.

Mentions: The degree of genetic interaction correlates with the number of different gene attributes [17]. In this study we investigated the relationship between the morphological extent in the gene deletion mutants and the number of genetic interactions. Stringent cutoff values were imposed to identify the genetic interaction in each gene (ϵ <−0.12, P <0.05 or ϵ >0.16, P <0.05). We found that >70% of the selected genes had >50 genetic interactions, with an average number of 180.0 (Figure 6), although about 50% of the randomly selected nonessential genes contained <50 genetic interactions. A Mann–Whitney U-test showed this difference to be statistically significant (P <0.01). These results suggested that the high morphological diversity of the heteroclite mutants was due to the impact of the genetic interaction.Figure 6


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

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

Distribution of the number of genetic interactions. (A) Alignment of the gene deletion strains according to the number of genetic interactions. Red and orange crosses indicate the detected strains and the undetected strains, respectively. The number of genetic interactions of 77 strains was counted, as the remainder was not available [17]. (B) Boxplot of the number of genetic interactions. Grey, red and orange boxes indicate number of genetic interactions in 100 genes randomly selected from nonessential genes as a reference, heteroclite strains and remaining strains, respectively. Gene number available for genetic interaction data is shown in parentheses.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Distribution of the number of genetic interactions. (A) Alignment of the gene deletion strains according to the number of genetic interactions. Red and orange crosses indicate the detected strains and the undetected strains, respectively. The number of genetic interactions of 77 strains was counted, as the remainder was not available [17]. (B) Boxplot of the number of genetic interactions. Grey, red and orange boxes indicate number of genetic interactions in 100 genes randomly selected from nonessential genes as a reference, heteroclite strains and remaining strains, respectively. Gene number available for genetic interaction data is shown in parentheses.
Mentions: The degree of genetic interaction correlates with the number of different gene attributes [17]. In this study we investigated the relationship between the morphological extent in the gene deletion mutants and the number of genetic interactions. Stringent cutoff values were imposed to identify the genetic interaction in each gene (ϵ <−0.12, P <0.05 or ϵ >0.16, P <0.05). We found that >70% of the selected genes had >50 genetic interactions, with an average number of 180.0 (Figure 6), although about 50% of the randomly selected nonessential genes contained <50 genetic interactions. A Mann–Whitney U-test showed this difference to be statistically significant (P <0.01). These results suggested that the high morphological diversity of the heteroclite mutants was due to the impact of the genetic interaction.Figure 6

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