Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.).
Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.).
复制标题
水稻 (Oryza sativa L.) 中自噬相关基因同源物的全基因组鉴定、分类和表达分析
DOI：
10.1093/dnares/dsr024
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发表时间：
2011-10
期刊：
影响因子：
--
通讯作者：
Zhang M
中科院分区：
文献类型：
--
作者：
Xia K;Liu T;Ouyang J;Wang R;Fan T;Zhang M
自噬是一种循环利用大分子和细胞器的细胞内降解过程。它在植物发育、营养需求、胁迫和衰老等方面发挥着重要作用。从酵母到植物的生物体都含有许多自噬相关基因（ATG）。在本研究中，我们发现水稻[Oryza sativa L. (Os)]基因组中共存在33个ATG同源物，它们被划分为13个ATG亚家族。其中六个是选择性剪接的基因。进化分析表明，10个OsATG同源物的扩增是通过片段重复事件发生的，并且这些同源物在每个亚家族中的发生是异步的。Ka/Ks比值表明纯化选择了4个重复的OsATG同源物，阳性选择了2个。计算复制事件的日期表明，所有的复制事件都可能发生在草的起源之后，从2143万年前到6677万年前。半定量RT-PCR分析和水稻数字表达数据库的挖掘表明，在正常或逆境生长条件下，所有33个OsATG同源基因都可以在多种组织的至少一种细胞类型中检测到，但它们的表达受到严格调控。10个重复基因表现出表达差异。大多数OsATG同源物的表达受到至少一种处理的调节，包括激素、非生物和生物胁迫以及营养限制。OsATG同源物的鉴定显示了构成性表达或对环境刺激的反应，为深入表征水稻中选定的重要基因提供了新的见解。
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.
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