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Author Lloyd J.P., Seddon A.E., Moghe G.D., Simenc M.C., Shiu S.H.
Title Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes.
Abstract:
Essential genes represent critical cellular components whose disruption results in lethality. Characteristics shared among essential genes have been uncovered in fungal and metazoan model systems. However, features associated with plant essential genes are largely unknown and the full set of essential genes remains to be discovered in any plant species. Here, we show that essential genes in Arabidopsis thaliana have distinct features useful for constructing within- and cross-species prediction models. Essential genes in A. thaliana are often single copy or derived from older duplications, highly and broadly expressed, slow evolving, and highly connected within molecular networks compared with genes with nonlethal mutant phenotypes. These gene features allowed the application of machine learning methods that predicted known lethal genes as well as an additional 1970 likely essential genes without documented phenotypes. Prediction models from A. thaliana could also be applied to predict Oryza sativa and Saccharomyces cerevisiae essential genes. Importantly, successful predictions drew upon many features, while any single feature was not sufficient. Our findings show that essential genes can be distinguished from genes with nonlethal phenotypes using features that are similar across kingdoms and indicate the possibility for translational application of our approach to species without extensive functional genomic and phenomic resources.
Journal Plant Cell
Country unknown
Volume
Pages
Year 2015
PubMed ID 26286535
PubMed Central ID -
DOI 10.1105/tpc.15.00051
URL -
Relation
Gene ADL1 ASB1 GELP112 MRP13 SHL2 SHL4 SHO1 SKIPA TATC VP1 WAF1 _ _ _ _ _ _ _
INSD -
Strain Wild Core Collection -
Induced Mutation Lines(NIG Collection) -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain
-
Stages in Each Organ
- Muant Lines (Gene)
-
Cultivated Varieties(NIG Collection) -
Stages in Each Organ -
/rice/oryzabase