樟树5种化学类型叶片转录组分析

doi:10.3724/SP.J.1005.2014.00058

遗传 ›› 2014, Vol. 36 ›› Issue (1): 58-68.doi: 10.3724/SP.J.1005.2014.00058

樟树5种化学类型叶片转录组分析

江香梅, 伍艳芳, 肖复明, 熊振宇, 徐海宁

江西省林业科学院, 国家林业局樟树工程技术研究中心, 南昌 330032

收稿日期:2013-04-25 修回日期:2013-07-23 出版日期:2014-01-20 发布日期:2013-12-20
通讯作者: 江香梅, 博士, 研究员。研究方向：林木遗传育种。E-mail: zjiang2013@126.com E-mail:zjiang2013@126.com
作者简介:江香梅, 博士, 研究员。研究方向：林木遗传育种。E-mail: zjiang2013@126.com
基金资助:
“赣鄱英才555工程”领军人才培养计划项目樟树全基因组研究和江西省自然科学基金项目(编号：20122BAB214029)资助

Transcriptome analysis for leaves of five chemical types in Cinna-momum camphora

Xiangmei Jiang, Yanfang Wu, Fuming Xiao, Zhenyu Xiong, Haining Xu

Camphor Engineering Technology Research Center for State Forestry Administration, Jiangxi Academy of Forestry, Nanchang 330032, China

Received:2013-04-25 Revised:2013-07-23 Online:2014-01-20 Published:2013-12-20

摘要/Abstract

摘要：

樟树(Cinnamomum camphora )是樟科植物的一个代表种, 具有材用、药用、香料、油用和生态环境建设等多种用途。叶精油中富含利用价值极高的樟脑、芳樟醇、1,8-桉叶油素、异-橙花叔醇和右旋龙脑等萜类化合物。依据叶精油中主要成分的种类和含量, 可将樟树划分为脑樟、芳樟、油樟、异樟、龙脑樟5种化学类型。文章采用Illumina HiSeq™ 2000高通量测序技术, 对5种化学类型叶片转录组进行测序, 对测序得到的所有Unigene进行GO(Gene Ontology)、COG(Clusters of Orthologous Groups)和KEGG(Kyoto Encyclopedia of Genes and Genomes)分类, 给出功能注释和Pathway注释, 并预测Unigene蛋白编码区(Coding sequence, CDS)。De novo组装共获得156 278个Unigene, 序列平均长度584 bp, N50(覆盖50%所有核苷酸的最大Unigene长度)为1 023 bp。通过与其他核酸、蛋白数据库的Blast搜索比对, 共有55 955条Unigene获得了基因注释, 占所有Unigene的35.80%。其中, 有24 717条Unigene得到GO注释, 有21 806条Unigene得到COG注释。KEGG pathways分析结果表明, 共有3 350条基因(10.19%)注释到次生代谢生物合成途径, 其中参与单萜、二萜、倍半萜和萜类骨架合成的Unigene有424个。在单萜合成的代谢通路中, 有9条Unigene可能编码芳樟醇合成酶基因, 且表达分析结果显示, 芳樟醇合成酶基因在芳樟化学类型中优势表达, 在油樟化学类型中表达水平较低。这些注释信息的完成为樟树功能基因及相关候选基因的发掘提供了基础数据和重要依据。

关键词: 樟树, RNA-Seq, 基因注释, 功能分类, CDS预测

Abstract:

Camphor tree (Cinnamomum camphora) is a representative species in Lauraceae family, and can be subdivided into five types: linalool, camphor, cineol, iso-nerolidol and borneol. In this paper, the leaves transcriptomes of Cinnamomum camphora were sequenced with the platform of Illumina HiSeq™ 2000. Based on the GO (Gene Ontology), COG (Clusters of Orthologous Groups), and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, the function classification, pathway annotation, and the coding sequence prediction of all-Unigenes were carried out. 156 278 Unigenes with an average length of 584 bp and N50 (N50 value is defined as the Unigene length where half the assembly is represented by Unigenes of this size or longer) of 1 023 bp were generated by de novo assembly. A total of 5 5955 Unigenes (35.80%) were annotated through similarity comparison, in which 24 717 and 21 806 Unigenes were assigned into GO and COG, respectively. By searching KEGG database, 3 350 Unigenes were involved in biosynthesis of secondary metabolites, in which 424 Unigenes were involved in monoterpenoids, diterpenoids, sesquiterpenoids, and terpenoid backbone biosynthesis. The analysis of monoterpenoids biosynthesis pathway showed that 9 Unigenes likely encode (+)-linalool synthase, and their expression levels were higher in linalool type but lower in cineole type. This study provides a foundation for further characterizing the functional genes in C. camphora.

Key words: Cinnamomum camphora, RNA-Seq, gene annotation, function classification, CDS prediction

江香梅, 伍艳芳, 肖复明, 熊振宇, 徐海宁. 樟树5种化学类型叶片转录组分析[J]. 遗传, 2014, 36(1): 58-68.

Xiangmei Jiang, Yanfang Wu, Fuming Xiao, Zhenyu Xiong, Haining Xu. Transcriptome analysis for leaves of five chemical types in Cinna-momum camphora[J]. HEREDITAS, 2014, 36(1): 58-68.

参考文献

[1] 戴宝合. 野生植物资源学. 北京: 农业出版社, 1993. <\p>

[2] 石皖阳, 何伟, 文光裕, 郭德选, 龙光远, 刘银苟. 樟精油成分和类型划分. 植物学报, 1989, 31(3): 209–214. <\p>

[3] 彭东辉. 樟树优良单株选择与组培研究<\p>

[学位论文]. 福建农林大学, 2004. <\p>

[4] Lee HJ, Hyuna EA, Yoon WJ, Kim BH, Rhee MH, Kang HK, Cho JY, Yoo ES. In vitro anti-inflammatory and an-ti-oxidative effects of Cinnamomum camphora extracts. J Ethnopharmacol, 2006, 103(2): 208–216. <\p>

[5] Liu CH, Mishra AK, Tan RX, Tang C, Yang H, Shen YF. Repellent and insecticidal activities of essential oils from Artemisia princeps and Cinnamomum camphora and their effect on seed germination of wheat and broad bean. Bio-resour Technol, 2006, 97(15): 1969–1973. <\p>

[6] Yang T, Li J, Wang HX, Zeng Y. A geraniol-synthase gene from Cinnamomum tenuipilum. Phytochemistry, 2005, 66(3): 285–293. <\p>

[7] 陈美兰. 药用植物樟化学型形成机理的基础研究<\p>

[学位论文]. 中国中医科学院, 2007. <\p>

[8] Zhang GJ, Guo GW, Hu XD, Zhang Y, Li QY, Li RQ, Zhang RH, Lu ZK, He ZQ, Fang XD, Chen L, Tian W, Tao Y, Kristiansen K, Zhang XQ, Li SG, Yang HM, Wang J. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res, 2010, 20(5): 646–654. <\p>

[9] Wu J, Zhang YL, Zhang HQ, Huang H, Folta KM, Lu J. Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa se-quencing technology. BMC Plant Biol, 2010, 10: 234. <\p>

[10] Guo SG, Zheng Y, Joung JG, Liu SQ, Zhang ZH, Crasta OR, Sobral BW, Xu Y, Huang SW, Fei ZJ. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010, 11: 384. <\p>

[11] Graham IA, Besser K, Blumer S, Branigan CA, Cze¬chowski T, Elias L, Guterman I, Harvey D, Isaac PG, Khan AM, Larson TR, Li Y, Pawson T, Penfield T, Rae AM, Rathbone DA, Reid S, Ross J, Swallwood MF, Segura V, Townsend T, Vyas D, Winzer T, Bowles D. The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug artemisinin. Science, 2010, 327(5963): 328–331. <\p>

[12] Chen S, Luo H, Li Y, Sun Y, Wu Q, Niu Y, Song J, Lv A, Zhu Y, Sun C, Steinmetz A, Qian Z. 454 EST analysis de-tects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. Plant Cell Rep, 2011, 30(9): 1593– 1601. <\p>

[13] Hao DC, Ge GB, Xiao PG, Zhang YY, Yang L. The first insight into the tissue specific Taxus transcriptome via Il-lumina second generation sequencing. PLoS ONE, 2011, 6(6): e21220. <\p>

[14] Tang Q, Ma XJ, Mo CM, Wilson IW, Song C, Zhao H, Yang YF, Fu W, Qiu DY. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics, 2011, 12(1): 343. <\p>

[15] Wilhelm BT, Landry JR. RNA-Seq quantitative measurement of expression through massively parallel RNA Sequencing. Methods, 2009, 48(3): 249–257. <\p>

[16] Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M. Charac-terization of transcriptional complexity during berry de-velopment in Vitis vinifera using RNA-Seq. Plant Physiol, 2010, 152(4): 1787–1795. <\p>

[17] Wang ZY, Fang BP, Chen JY, Zhang XJ, Luo ZX, Huang LF, Chen XL, Li YJ. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpo¬tato (Ipomoea batatas). BMC Genomics, 2010, 11(1): 726. <\p>

[18] 李滢, 孙超, 罗红梅, 李西文, 牛云云, 陈士林. 基于高通量测序454 GS FLX的丹参转录组学研究. 药学学报, 2010, 45(4): 524–529. <\p>

[19] Sun C, Li Y, Wu Q, Luo HM, Sun YZ, Song JY, Lui E MK, Chen SL. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative ge

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

樟树5种化学类型叶片转录组分析

Transcriptome analysis for leaves of five chemical types in Cinna-momum camphora

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 10

编辑推荐

Metrics

[1]	杜坤, 毛初阳, 任安勇, 吴雪梅, 李庆玲, 陈婷婷, 陈仕毅, 赖松家. 家兔前体脂肪细胞分化不同时期基因表达谱分析[J]. 遗传, 2020, 42(3): 309-320.
[2]	魏金川,徐添翼,吴静,宋晓峰. 真核生物基因组长内含子递归剪接事件的分子机制[J]. 遗传, 2019, 41(2): 89-97.
[3]	张宇,白素英,马跃. 麝鼠前列腺在繁殖期和非繁殖期转录组差异分析[J]. 遗传, 2018, 40(6): 488-495.
[4]	黄万龙,张秀秀,李嫒,苗向阳. 利用RNA-seq技术筛选大白猪皮下和肌内脂肪组织差异表达基因[J]. 遗传, 2017, 39(6): 501-511.
[5]	文路, 汤富酬. 单细胞转录组高通量测序分析新进展[J]. 遗传, 2014, 36(11): 1069-1076.
[6]	侯志伟王赟高宏侯圣伟. dRNA-seq原理及其在原核生物转录组学研究中的应用[J]. 遗传, 2013, 35(8): 983-991.
[7]	刘红亮郑丽明刘青青权富生张涌. 非模式生物转录组研究[J]. 遗传, 2013, 35(8): 955-970.
[8]	陈昊蒋桂雄龙洪旭谭晓风. 基于油桐种子3个不同发育时期转录组的油脂合成代谢途径分析[J]. 遗传, 2013, 35(12): 1403-1414.
[9]	刘喜冬，王志鹏，樊惠中，李俊雅，高会江. 基于高密度SNP标记的肉牛人工选择痕迹筛查[J]. 遗传, 2012, 34(10): 1304-1313.
[10]	祁云霞，刘永斌，荣威恒. 转录组研究新技术：RNA-Seq及其应用[J]. 遗传, 2011, 33(11): 1191-1202.