Genome-Wide Identification, Classification, and Expression Analysis of Autophagy-Associated Gene Homologues in Rice (Oryza sativa L.)
Open Access
- 27 July 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in DNA Research
- Vol. 18 (5), 363-377
- https://doi.org/10.1093/dnares/dsr024
Abstract
Autophagy is an intracellular degradation process for recycling macromolecules and organelles. It plays important roles in plant development and in response to nutritional demand, stress, and senescence. Organisms from yeast to plants contain many autophagy-associated genes (ATG). In this study, we found that a total of 33 ATG homologues exist in the rice [Oryza sativa L. (Os)] genome, which were classified into 13 ATG subfamilies. Six of them are alternatively spliced genes. Evolutional analysis showed that expansion of 10 OsATG homologues occurred via segmental duplication events and that the occurrence of these OsATG homologues within each subfamily was asynchronous. The Ka/Ks ratios suggested purifying selection for four duplicated OsATG homologues and positive selection for two. Calculating the dates of the duplication events indicated that all duplication events might have occurred after the origin of the grasses, from 21.43 to 66.77 million years ago. Semi-quantitative RT–PCR analysis and mining the digital expression database of rice showed that all 33 OsATG homologues could be detected in at least one cell type of the various tissues under normal or stress growth conditions, but their expression was tightly regulated. The 10 duplicated genes showed expression divergence. The expression of most OsATG homologues was regulated by at least one treatment, including hormones, abiotic and biotic stresses, and nutrient limitation. The identification of OsATG homologues showing constitutive expression or responses to environmental stimuli provides new insights for in-depth characterization of selected genes of importance in rice.Keywords
This publication has 42 references indexed in Scilit:
- RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditionsNucleic Acids Research, 2010
- Autophagy in plants and phytopathogensFEBS Letters, 2010
- The Pfam protein families databaseNucleic Acids Research, 2009
- Autophagy Negatively Regulates Cell Death by Controlling NPR1-Dependent Salicylic Acid Signaling during Senescence and the Innate Immune Response inArabidopsisPlant Cell, 2009
- An Overview of the Molecular Mechanism of AutophagyCurrent topics in microbiology and immunology, 2009
- The ATG Autophagic Conjugation System in Maize: ATG Transcripts and Abundance of the ATG8-Lipid Adduct Are Regulated by Development and Nutrient AvailabilityPlant Physiology, 2008
- Rice–arsenate interactions in hydroponics: whole genome transcriptional analysisJournal of Experimental Botany, 2008
- Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome EvolutionPlant Cell, 2008
- An Arabidopsis Homolog of YeastATG6/VPS30Is Essential for Pollen GerminationPlant Physiology, 2007
- A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue CulturesPhysiologia Plantarum, 1962