Plant Genome Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan.
Gene. 2010 Oct 1;465(1-2):30-44. doi: 10.1016/j.gene.2010.06.008. Epub 2010 Jun 26.
We investigated 151 non-redundant NAC genes in rice and 117 in Arabidopsis. A complete overview of this gene family in rice is presented, including gene structures, phylogenies, genome localizations, and expression profiles. We also performed a comparative analysis of these genes in rice and Arabidopsis. Conserved amino acid residues and phylogeny construction using the NAC conserved domain sequence suggest that OsNAC gene family was classified broadly into two major groups (A and B) and sixteen subgroups in rice. We presented more specific phylogenetic analysis of OsNAC proteins based on the DNA-binding domain and known gene function, respectively. Loss of introns was observed in the segmental duplication. Homologous, paralogous, and orthologous searches of rice and Arabidopsis revealed that the major functional diversification within the NAC gene family predated the divergence of monocots and dicots. The chromosomal localizations of OsNAC genes indicated nine segmental duplication events involving 18 genes; 32 non-redundant OsNAC genes were involved in tandem duplications. Expression levels of this gene family were checked under various abiotic stresses (cold, drought, submergence, laid-down submergence, osmotic, salinity and hormone) and biotic stresses [infection with rice viruses such as RSV (rice stripe virus) and RTSV (rice tungro spherical virus)]. Biotic stresses are novel work and increase the possibilities for finding the best candidate genes. A preliminary search based on our microarray (22K and 44K) data suggested that more than 45 and 26 non-redundant genes in this family were upregulated in response to abiotic and biotic stresses, respectively. All of the genes were further investigated for their stress responsiveness by RT-PCR analysis. Six genes showed preferential expression under both biotic RSV and RTSV stress. Eleven genes were upregulated by at least three abiotic treatments. Our study provides a very useful reference for cloning and functional analysis of members of this gene family in rice.
我们研究了水稻中的 151 个非冗余 NAC 基因和拟南芥中的 117 个 NAC 基因。本文全面介绍了水稻 NAC 基因家族，包括基因结构、系统发育、基因组定位和表达谱。我们还对水稻和拟南芥中的这些基因进行了比较分析。保守氨基酸残基和基于 NAC 保守结构域序列的系统发育构建表明，OsNAC 基因家族在水稻中广泛分为两大组（A 和 B）和十六个亚组。我们根据 DNA 结合域和已知基因功能分别对 OsNAC 蛋白进行了更具体的系统发育分析。在片段重复中观察到内含子的丢失。对水稻和拟南芥的同源、旁系和直系同源搜索表明，NAC 基因家族的主要功能多样化发生在单子叶植物和双子叶植物分化之前。OsNAC 基因的染色体定位表明，涉及 18 个基因的 9 个片段重复事件；32 个非冗余 OsNAC 基因参与串联重复。该基因家族的表达水平在各种非生物胁迫（冷、干旱、淹没、淹水、渗透、盐度和激素）和生物胁迫（感染水稻病毒如 RSV（水稻条纹病毒）和 RTSV（水稻曲叶病毒））下进行了检测。生物胁迫是一项新的工作，增加了寻找最佳候选基因的可能性。基于我们的微阵列（22K 和 44K）数据的初步搜索表明，该家族中有超过 45 个和 26 个非冗余基因分别对非生物和生物胁迫有上调表达。所有的基因都通过 RT-PCR 分析进一步研究了它们的应激反应性。6 个基因在生物胁迫 RSV 和 RTSV 下均表现出优先表达。11 个基因至少被三种非生物处理上调。我们的研究为克隆和功能分析水稻中该基因家族的成员提供了非常有用的参考。
