Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa.
Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa.
复制标题
毛果杨NAC结构域转录因子基因家族的综合分析
DOI：
10.1186/1471-2229-10-145
复制
发表时间：
2010-07-15
影响因子：
5.3
通讯作者：
Zhou G
中科院分区：
文献类型：
--
作者：
Hu R;Qi G;Kong Y;Kong D;Gao Q;Zhou G
背景
NAC(NAM，ATAF1/2和CUC2)结构域蛋白是已知在植物发育过程中发挥不同作用的植物特有的转录因子。NAC转录因子由一个大的基因家族组成，在拟南芥、水稻和大豆等植物中有100多个成员。最近，人们对11种植物的NAC基因家族进行了初步的系统发育分析。然而，到目前为止，还没有关于模式树种杨树的系统发育、染色体位置、基因结构、保守基序和表达谱分析的全面研究。
结果
本研究对杨树NAC基因家族进行了综合分析。在杨属植物中共鉴定出163个全长NAC基因，它们在系统发育上聚为18个亚科。亚家族间的基因结构和基序组成具有较高的保守性。在19个连锁群中，120个杨树NAC基因的分布是非随机的，其中87个基因(73%)优先保留位于两个重复区域的重复。根据EST频率和微阵列数据分析，大多数NAC显示出特定的时间和空间表达模式。然而，大多数重复基因的表达模式是部分冗余的，这表明在随后的进化过程中发生了亚功能化。采用实时定量RT-PCR(RT-qPCR)技术对25个NAC基因的组织特异性表达模式进行了验证。
结论
根据基因组结构，我们可以得出结论，节段性复制对杨树NAC基因家族的扩大起到了重要作用。全面的表达谱分析首次揭示了NAC基因家族成员之间的功能差异。此外，节段复制后表达模式的高分歧率表明，杨树中的NAC基因同样被大量的亚功能化所保留。综上所述，我们的结果将有助于为NAC基因家族的功能鉴定奠定基础，并进一步了解这些家族成员之间的结构-功能关系。
Background
NAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.
Results
In the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.
Conclusion
Based on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.
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NACL胁迫的拟南芥根的全面转录分析揭示了新的反应基因类别。
影响因子：
5.3
作者：
Jiang, Yuanqing;Deyholos, Michael K.
通讯作者：
Deyholos, Michael K.
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
5.1
作者：
Collinge, M;Boller, T
通讯作者：
Boller, T
DOI：
10.1007/pl00008647
发表时间：
2000-01-01
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
Kikuchi, K;Ueguchi-Tanaka, M;Hirano, HY
通讯作者：
Hirano, HY
影响因子：
7.2
作者：
Kim, Sang-Gyu;Lee, An-Kyo;Park, Chung-Mo
通讯作者：
Park, Chung-Mo