巨桉AGO基因家族的生物信息学分析
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中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所,中国林业科学研究院热带林业研究所

基金项目:

国家"863"高技术研究发展计划(2013AA102705); 国家自然科学基金项目(31400554); 中央级公益性科研院所基本科研业务费专 项(RITFYWZX201304)资助


Bioinformatics Analysis of AGO Gene Family in Eucalyptus grandis Genome
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Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520,Research Institute of Tropical Forestry,chinese Academy of Forestry,Guangzhou,510520

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    摘要:

    为了解巨桉(Eucalyptus grandis)中Argonaute (AGO)的功能, 经全基因组序列分析, 巨桉中存在14 个AGO基因家族成员, 基因长度为2676~3225 bp, 编码的蛋白质具有保守的Piwi、PAZ、DUF1785 结构域。巨桉EgrAGOs 基因可分为3 组, 内含子和外显子结构具有明显的组织特异性。组内成员核苷酸序列和氨基酸序列保守性较高, 同源性分别达到88.14% 和82.97%。EgrAGO基因分布于第2、4、7、8、10、11 条染色体上, 在进化过程中存在着串联复制和大片段基因复制机制。预测巨桉的大部分AGO 蛋白定位于细胞核和胞质中, 表现出偏碱性和亲水性, 具有较高的脂溶指数。基因表达分析表明, 桉树EgrAGO成员在不同组织中的表达有明显差异, 与木材形成相关的组织/ 器官中有较高的表达。这些为深入研究EgrAGO基因的功能奠定了基础。

    Abstract:

    In order to understand the function of Argonaute (AGO) in Eucalyptus grandis, the phylogeny, gene structure and expression pattern of EgrAGO were analyzed in genome-wide. The results showed that there were 14 EgrAGOs in E. grandis, which length ranged from 2676 to 3225 bp and EgrAGOs contain Piwi, PAZ and DUF1785 domains. EgrAGO genes could be divided into 3 clades, and intron and exon structures had obvious tissue specificity. The nucleotide sequence of EgrAGO and encoding amino acid sequence in each clade had homologies for 88.14% and 82.97%, respectively. Meanwhile, EgrAGO genes distribute in 2, 4, 7, 8, 10 and 11 chromosomes with tandem duplication and segmental duplication in the process of evolution. Most of EgrAGO proteins localize in nucleus and cytoplasm, showing basicity, hydrophilia and high aliphatic index. Furthermore, the expression of EgrAGOs in different tissues had significant differences, and which was high in tissues or organs related with wood forming. So, these would lay a fundation for studying EgrAGO genes function in future.

    参考文献
    [1] Tolia N H, Joshua-Tor L. Slicer and the argonautes [J]. Nat Chem Biol, 2007, 3(1): 36-43.
    [2] Ghildiyal M, Zamore P D. Small silencing RNAs: An expanding universe [J]. Nat Rev Genet, 2009, 10(2): 94-108.
    [3] Cenik E S, Zamore P D. Argonaute proteins [J]. Curr Biol, 2011, 21(12): R446-R449.
    [4] Mi S J, Cai T, Hu Y G, et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide [J]. Cell, 2008, 133(1): 116-127.
    [5] Mallory A, Vaucheret H. Form, function, and regulation of ARGONAUTE proteins [J]. Plant Cell, 2010, 22(12): 3879-3889.
    [6] Vaucheret H. Plant ARGONAUTES [J]. Trends Plant Sci, 2008, 13(7): 350-358.
    [7] Sha A H, Zhao J P, Yin K Q, et al. Virus-based MicroRNA silencing in plants [J]. Plant Physiol, 2014, 164(1): 36-47.
    [8] Fernández-Nohales P, Domenech M J, de Alba A E M, et al. AGO1 controls arabidopsis inflorescence architecture possibly by regulating TFL1 expression [J]. Ann Bot, 2014, 114(7): 1471-1481.
    [9] Zhu H L, Hu F Q, Wang R H, et al. Arabidopsis argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development [J]. Cell, 2011, 145(2): 242-256.
    [10] Li C F, Pontes O, El-Shami M, et al. An ARGONAUTE4-containing nuclear processing center colocalized with cajal bodies in Arabidopsis thaliana [J]. Cell, 2006, 126(1): 93-106.
    [11] Zheng X W, Zhu J H, Kapoor A, et al. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing [J]. EMBO J, 2007, 26(6): 1691-1701.
    [12] Cuperus J T, Fahlgren N, Carrington J C. Evolution and functional diversification of MIRNA genes [J]. Plant Cell, 2011, 23(2): 431-442.
    [13] Montgomery T A, Howell M D, Cuperus J T, et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation [J]. Cell, 2008, 133(1): 128-141.
    [14] Wang H, Zhang X R, Liu J, et al. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions [J]. Plant J, 2011, 67(2): 292-304.
    [15] Myburg A A, Grattapaglia D, Tuskan G A, et al. The genome of Eucalyptus grandis [J]. Nature, 2014, 510(7505): 356-362.
    [16] Yang Y, Zhong J, Ouyang Y D, et al. The integrative expression and co-expression analysis of the AGO gene family in rice [J]. Gene, 2013, 528(2): 221-235.
    [17] Ji L J, Liu X G, Yan J, et al. ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis [J]. PLoS Genet, 2011, 7(3): e1001358.
    [18] Minoia S, Carbonell A, Di Serio F, et al. Specific ARGONAUTES selectively bind small RNAs derived from potato spindle tuber viroid and attenuate viroid accumulation in vivo [J]. J Virol, 2014, 88(20): 11933-11945.
    [19] Baumberger N, Baulcombe D C. Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs [J]. Proc Natl Acad Sci USA, 2005, 102(33): 11928-11933.
    [20] Kidner C A, Martienssen R A. The role of ARGONAUTE1 (AGO1) in meristem formation and identity [J]. Dev Biol, 2005, 280(2): 504-517.
    [21] Yang L, Huang W, Wang H, et al. Characterizations of a hypomorphic argonaute1 mutant reveal novel AGO1 functions in Arabidopsis lateral organ development [J]. Plant Mol Biol, 2006, 61(1/2): 63-78.
    [22] Li W, Cui X, Meng Z L, et al. Transcriptional regulation of Arabidopsis MIR168a and ARGONAUTE1 homeostasis in abscisic acid and abiotic stress responses [J]. Plant Physiol, 2012, 158(3): 1279-1292.
    [23] Lynn K, Fernandez A, Aida M, et al. The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene [J]. Development, 1999, 126(3): 469-481.
    [24] Bai M, Yang G S, Chen W T, et al. Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum [J]. Gene, 2012, 501(1): 52-62.
    [25] Xian Z Q, Huang W, Yang Y W, et al. miR168 influences phase transition, leaf epinasty, and fruit development via SlAGO1s in tomato [J]. J Exp Bot, 2014, 65(22): 6655-6666.
    [26] Xu M, Xie W F, Pan H X, et al. Cloning and characterization of ARGONAUTE genes in Populus [J]. Sci Silv Sin, 2011, 47(3): 46-51. 胥猛谢雯凡, 潘惠新, 等. 杨树ARGONAUTE基因的克隆及序列分析 [J]. 林业科学, 2011, 47(3): 46-51.
    [27] Robischon M, Du J, Miura E, et al. The Populus class Ⅲ HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems [J]. Plant Physiol, 2011, 155(3): 1214-1225.
    [28] Ohashi-Ito K, Fukuda H. Transcriptional regulation of vascular cell fates [J]. Curr Opin Plant Biol, 2010, 13(6): 670-676.
    [29] Ye R Q, Wang W, Iki T, et al. Cytoplasmic assembly and selective nuclear import of Arabidopsis ARGONAUTE4/siRNA complexes [J]. Mol Cell, 2012, 46(6): 859-870.
    [30] Li C H, Chiang C P, Yang J Y, et al. RING-type ubiquitin ligase McCPN1 catalyzes UBC8-dependent protein ubiquitination and interacts with Argonaute 4 in halophyte ice plant [J]. Plant Physiol Biochem, 2014, 80: 211-219.
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范春节,闫慧芳,裘珍飞,曾炳山,刘英,李湘阳,王象军,郭光生.巨桉AGO基因家族的生物信息学分析[J].热带亚热带植物学报,2015,23(4):361~369

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  • 收稿日期:2014-10-09
  • 最后修改日期:2015-01-09
  • 录用日期:2015-02-12
  • 在线发布日期: 2015-07-15
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