Genome-wide Identification and Expression Analysis of NCED Gene Family in Phyllostachys edulis
XU Yin1, HU Qiu-Tao1, HOU Dan1, LU Hai-Wen1, LIN Xin-Chun1,2,*
1 State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; 2 Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Hangzhou, 311300, China
Abstract：9-cis-epoxycarotenoid dioxygenase (NCED) is the key rate-limiting enzyme in abscisic acid (ABA) biosynthesis pathway. In this study, bioinformatics method was used to identify 10 genes with complete NCED conserved domain RPE65 from the whole genome of Phyllostachys edulis. The length of the NCED proteins ranged from 240 to 654 aa with molecular mass of 28.03 to 70.04 kD. Phylogenetic analysis showed that the 10 NCED genes could be divided into 2 subgroups, and most NCED genes were closely related to rice (Oryza sativa) NCED genes, except for PH02Gene49300 and PH02Gene41427. The predictive analysis of cis-acting elements showed that NCED gene promoter contained a large number of abiotic stress response elements, indicating that they might play an important role in the stress resistance of Ph. edulis. Transcriptome data analysis showed that the expression of NCED genes in different tissues and developmental stages of Ph. edulis was specific, especially highly expressed in the roots and shoots (P<0.05). The qRT-PCR results showed that NCED genes had different expression patterns under ABA, salicylic acid (SA), drought and salt stress treatments, which suggested that NCEDs might play different roles in the regulation of stress and hormones response. The present work provides a basic data for further study of the function of NCED gene family in Phyllostachys edulis.
徐胤, 胡秋涛, 侯丹, 鲁海雯, 林新春. 毛竹NCED基因家族的全基因组鉴定及表达分析[J]. 农业生物技术学报, 2021, 29(6): 1061-1072.
XU Yin, HU Qiu-Tao, HOU Dan, LU Hai-Wen, LIN Xin-Chun. Genome-wide Identification and Expression Analysis of NCED Gene Family in Phyllostachys edulis. 农业生物技术学报, 2021, 29(6): 1061-1072.
[1] 白羽聪, 李翔宇, 程占超, 等. 2019. 毛竹PIN基因家族的鉴定与生物信息学分析[J]. 分子植物育种, 17(16): 5238-5247. (Bai Y C, Li X Y, Chen Z C, et al.2019. Identification and bioinformatics analysis of PIN gene family in moso bamboo (Phyllostachys edulis)[J]. Molecular Plant Breeding, 17(16): 5238-5247.) [2] 程占超, 侯丹, 马艳军, 等. 2017. 毛竹生长素反应因子基因的生物信息学分析及差异表达[J]. 浙江农林大学学报, 34(04): 574-580. (Cheng Z C, Hou D, Ma Y J, et al.2017. Bioinformatic analysis and differential expression of auxin response factor (ARF) gene in Phyllostachys edulis[J]. Journal of Zhejiang A & F University, 34(4): 574-580.) [3] 胡秋涛, 侯丹, 赵钟毓, 等. 2020.毛竹PP2C基因家族鉴定与表达分析[J]. 农业生物技术学报, 28(10): 1776-1787. (Hu Q T, Hou D, Zhao Z Y, et al.2020. Identification and expression analysis of PP2C gene family in Phyllostachys edulis[J]. Journal of Agricultural Biotechnology, 28(10): 1776-1787.) [4] 李保珠, 安国勇, 韩栓. 2012. 植物激素ABA在水分胁迫下的功能及信号途径[J]. 植物生理学报, 48(01): 11-18. (Li B Z, An G Y, Han S.2012. Function and signaling of plant hormone ABA under water stress[J]. Plant Physiology Journal, 48(01): 11-18.) [5] 梁超琼, 孟嫣, 罗来鑫, 等. 2015. 基于复制酶基因序列的黄瓜绿斑驳花叶病毒系统进化及生物信息学分析[J]. 病毒学报, 31(6): 620-628. (Liang C Q, Meng M, Luo L X, et al.2015. Phylogenetic analysis and bioinformatics analysis of Cucumber green marker mosaic virus based on replicase gene sequences[J]. Chinese Journal of Virology, 31(6): 620-628.) [6] 潘春柳, 姚绍嫦, 黄燕芬, 等. 2020. 草果AtNCED基因克隆、表达和植物表达载体构建[J]. 分子植物育种, 18(05): 1520-1528. (Pan C L, Yao S E, Huang Y F.2020. Cloning, expression and plant expression vector construction of AtNCED gene from Amomum tsaoko[J]. Molecular Plant Breeding, 18(05): 1520-1528. ) [7] 佘奎军, 许志斌, 李新, 等. 2010. 玉米NCED基因的序列特征及生物信息学分析[J]. 宁夏农林科技, (05): 14-17. (She K J, Xu Z B, Li X, et al. 2010. Sequence features and bioinformatics analysis of NCED gene in Zea mays[J]. Ningxia Agriculture and Forestry Science and Technology, (05): 14-17.) [8] 苏海兰, 周先治, 李希, 等. 2018. 云南重楼种子萌发过程内源激素含量及酶活性变化研究[J]. 核农学报, 32(01): 141-149. (Su H L, Zhou X Z, Li X, et al.2018. Dynamic changes of enzyme and endogenous of Paris polyphylla Smith var. yunnanensis seed during different stages of germination[J]. Journal of Nuclear Agricultural Sciences, 32(01): 141-149.) [9] 王小龙, 刘凤之, 史祥宾,等. 2019. 葡萄NCED基因家族进化及表达分析[J]. 植物学报, 54(04): 474-485. (Wang X L, Liu F Z, Shi X B, et al.2019. Evolution and expression of NCED family genes in Vitis vinifera[J]. Chinese Bulletin of Botany, 54(04): 474-485.) [10] 王玉霞, 毛婵娟, 丁佳琳, 等. 2018. 水稻OsNCED3基因突变延缓叶片衰老[J]. 复旦学报(自然科学版), 57(6): 749-756, 766. (Wang Y X, Mao C J, Ding J L, et al.2018. Mutation of rice OsNCED3 gene delay the senescence of rice leaf[J]. Journal of Fudan University (Natural Science), 57(6): 749-756, 766.) [11] 吴佳军, 俞率成, 刘志刚, 等. 2019. 毛竹B3家族全基因组鉴定及表达模式分析[J]. 农业生物技术学报, 27(01): 43-54. (Wu J J, Yu S C, Liu Z G, et al.2019. Genome identification and expression pattern analysis of Phyllostachys edulis B3 family[J]. Journal of Agricultural Biotechnology, 27(1): 43-54.) [12] 吴林军, 张智俊, 朱丰晓, 等. 2018. 毛竹qRT-PCR分析中内参基因的选择[J]. 农业生物技术学报, 26(3): 502-510. (Wu L J, Zhang Z J, Zhu F X, et al.2018. The selection of endogenous reference genes in Phyllostachys edulis for qRT-PCR analysis[J]. Journal of Agricultural Biotechnology, 26(3): 502-510.) [13] 西廷业. 2008. 小麦TaNCED1基因的表达载体构建及功能分析[D]. 硕士学位论文, 山东农业大学, 导师: 刘树兵, 王洪刚, pp. 41-45. (Xi T Y.2008. Construction of expression vector and functional analysis of the Triticum aestivum L. TaNCED1 genes[D]. Thesis for M.D., Shandong Agricultural University, Supervisor: Liu S B, Wang H G, pp. 41-45.) [14] 徐学中, 汪婷, 万旺, 等. 2018. 水稻ABA生物合成基因OsNCED3响应干旱胁迫[J]. 作物学报, 44(01): 24-31. (Xu X Z, Wang T, Wan W, et al.2018. ABA biosynthesis gene OsNCED3 confers drought stress tolerance in rice[J]. Acta Agronomica Sinica, 44(01): 24-31.) [15] 赵钟毓, 侯丹, 胡秋涛, 等. 2020. 毛竹PeNAC047基因的克隆与表达分析[J]. 农业生物技术学报, 28(01): 58-71. (Zhao Z Y, Hou D, Hu Q T, et al.2020. Cloning and expression analysis of PeNAC047 gene from Phyllostachys edulis[J]. Journal of Agricultural Biotechnology, 28(1): 58-71.) [16] 周丽, 李梦婷, 朱骞, 等. 2020. 水稻OsNCED4基因的克隆及功能初探[J]. 分子植物育种, 18(07): 2087-2096. (Zhou L, Li M T, Zhu Q, et al.2020. Cloning and function analysis of OsNCED4 gene in rice[J]. Molecular Plant Breeding, 18(07): 2087-2096.) [17] Ahrazem O, Rubio-Moraga A, Trapero A, et al.2012. Developmental and stress regulation of gene expression for a 9-cis-epoxycarotenoid dioxygenase, CstNCED, isolated from Crocus sativus stigmas[J]. Journal of Experimental Botany, 63(2): 681-694. [18] Chen P, Sun Y F, Kai W B, et al.2016. Interactions of ABA signaling core components (SlPYLs, SlPP2Cs, and SlSnRK2s) in tomato (Solanum lycopersicon)[J]. Journal of Plant Physiology, 205(1): 67-74. [19] Chernys J T, Zeevaart C J A D.2000. Characterization of the 9-cis-epoxycarotenoid dioxygenase gene family and the regulation of abscisic acid biosynthesis in avocado[J]. Plant Physiology, 124(1): 343-353. [20] Frey A, Effroy D, Lefebvre V, et al.2012. Epoxycarotenoid cleavage by NCED5 fine-tunes ABA accumulation and affects seed dormancy and drought tolerance with other NCED family members[J]. The Plant Journal, 70(3): 501-512. [21] Fujita Y, Fujita M, Shinozaki K, et al.2011. ABA-mediated transcriptional regulation in response to osmotic stress in plants[J]. Journal of Plant Research, 124(4): 509-525. [22] Gao Z M, Li X P, Li L B, et al.2006. An effective method fortotal RNA isolation from bamboo[J]. Chinese Forestry Science and Technology, 5(3): 52-54. [23] Huang Y, Yang J, Xie N K, et al.2019. OsNCED5, a 9-cis-epoxycarotenoid dioxygenase gene, regulates salt and water stress tolerance and leaf senescence in rice[J]. Plant Science, 287: 110188. [24] Hwang, S G, Chen H C, Huang W Y, et al.2010. Ectopic expression of rice OsNCED3 in Arabidopsis increases ABA level and alters leaf morphology[J]. Plant Science, 178(1): 12-22. [25] Iuchi S, Masatomo K, Taji T, et al.2001. Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis[J]. The Plant Journal, 27(4): 325-333. [26] Maarten K, Karen M L, Schwartz S H, et al.1998. The genetic and molecular dissection of abscisic acid biosynthesis and signal transduction in Arabidopsis[J]. Plant Physiology and Biochemistry, 36(1/2): 83-89. [27] Neill S J, Burnett E C, Desikan R, et al.1998. Cloning of a wilt-responsive cDNA from an Arabidopsis thaliana suspension culture cDNA library that encodes a putative 9-cis-epoxy-carotenoid dioxygenase[J]. Journal of Experimental Botan, 328(49): 1893-1894. [28] Priya R, Siva R.2015. Analysis of phylogenetic and functional diverge in plant nine-cis epoxycarotenoid dioxygenase gene family[J]. Journal of Plant Research, 128(4): 519-534. [29] Qin X, Zeevaart J A D.1999. The 9-cis-epoxycarotenoid cleavage reaction is the key regulatory step of abscisic acid biosynthesis in water-stressed bean[J]. Proceedings of the National Academy of Sciences of the USA, 96(26): 15354-15361. [30] Rodrigo M, Alquezar B, Zacarías L.2006. Cloning and characterization of two 9-cis-epoxycarotenoid dioxygenase genes, differentially regulated during fruit maturation and under stress conditions, from orange (Citrus sinensis L. Osbeck)[J]. Journal of Experimental Botany, 53(3): 633-643. [31] Tan B C, Josephy L M, Dengy W T, et al.2010. Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family[J]. Plant Journal for Cell & Molecular Biology, 35(1): 44-56. [32] Tan B C, Mccarty D R.1997. Genetic control of abscisic acid biosynthesis in maize[J]. Proceedings of the National Academy of Sciences of the USA, 94(22): 12235-12240. [33] Thompson A J, Jackson A C, Symonds R C, et al.2010. Ectopic expression of a tomato 9-cis-epoxycarotenoid dioxygenase gene causes over-production of abscisic acid[J]. Plant Journal, 23(3): 363-374. [34] Trivellini A, Ferrante A, Vernieri P, et al.2011. Effects of promoters and inhibitors of ethylene and ABA on flower senescence of Hibiscus rosa-sinensis L.[J]. Journal of Plant Growth Regulation, 30(2): 175-184. [35] Valérie L, North H, Frey A, et al.2010. Functional analysis of Arabidopsis NCED6 and NCED9 genes indicates that ABA synthesized in the endosperm is involved in the induction of seed dormancy[J]. Plant Journal for Cell & Molecular Biology, 45(3): 309-319. [36] Yuan H, Yiming G, Yuting L, et al.2018. 9-cis-epoxycarotenoid dioxygenase 3 regulates plant growth and enhances multi-abiotic stress tolerance in rice[J]. Frontiers in Plant Science, 9(162): 1-18. [37] Zhao H, Gao Z, Wang L, et al.2018. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)[J]. GigaScience, 7(10). DOI: 10.1093/gigascience/giy115. [38] Zong W, Tang N, Yang J, et al.2016. Feedback regulation of ABA signaling and biosynthesis by a bZIP transcription factor targets drought-resistance-related genes[J]. Plant physiology, 171(4): 2810-2825.
