Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha

BMC Genomics

Long-Fang O Chen¹  Shih-Tong Jeng⁵  Hsiao-Feng Lo³  Chien-Yu Chen⁴  Li-Chun Huang¹  Mei-Ju Chu¹  Ting-Ying Chien²  Meng-Han Yang⁶  Tony Chien-Yen Kuo⁷  Chuan-Hung Chen⁵ 

[1] Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei 11529, Taiwan;Department of Computer Science and Information Engineering, National Taiwan University, Kaohsiung 811, Taiwan;Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan;Center of Systems Biology, National Taiwan University, Taipei 106, Taiwan;Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan;Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 811, Taiwan;Department of Bio-industrial Mechatronics Engineering, National Taiwan University, Taipei 106, Taiwan

关键词: Genome;    Aquilaria;    Cucurbitacin;    Agarwood;   

Others  :  856560
DOI  :  10.1186/1471-2164-15-578

 received in 2013-10-24, accepted in 2014-07-01,  发布年份 2014

【 摘 要 】

Background

Agarwood is derived from Aquilaria trees, the trade of which has come under strict control with a listing in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Many secondary metabolites of agarwood are known to have medicinal value to humans, including compounds that have been shown to elicit sedative effects and exhibit anti-cancer properties. However, little is known about the genome, transcriptome, and the biosynthetic pathways responsible for producing such secondary metabolites in agarwood.

Results

In this study, we present a draft genome and a putative pathway for cucurbitacin E and I, compounds with known medicinal value, from in vitro Aquilaria agallocha agarwood. DNA and RNA data are utilized to annotate many genes and protein functions in the draft genome. The expression changes for cucurbitacin E and I are shown to be consistent with known responses of A. agallocha to biotic stress and a set of homologous genes in Arabidopsis thaliana related to cucurbitacin bio-synthesis is presented and validated through qRT-PCR.

Conclusions

This study is the first attempt to identify cucurbitacin E and I from in vitro agarwood and the first draft genome for any species of Aquilaria. The results of this study will aid in future investigations of secondary metabolite pathways in Aquilaria and other non-model medicinal plants.

【 授权许可】

   
2014 Chen et al.; licensee BioMed Central Ltd.

【 图 表 】

【 参考文献 】

• [1]Chen HQ, Wei JH, Yang JS, Zhang Z, Yang Y, Gao ZH, Sui C, Gong B: Chemical constituents of agarwood originating from the endemic genus Aquilaria plants. Chem Biodivers 2012, 9:236-250.
• [2]Liu YY, Chen HQ, Yang Y, Zhang Z, Wei JH, Meng H, Chen WP, Feng JD, Gan BC, Chen XY, Gao ZH, Huang JQ, Chen B, Chen HJ: Whole-tree Agarwood-Inducing Technique: An Efficient Novel Technique for Producing High-Quality Agarwood in Cultivated Aquilaria sinensis Trees. Molecules 2013, 18:3086-3106.
• [3]Ueda J, Imamura L, Tezuka Y, Tran QL, Tsuda M, Kadota S: New sesquiterpene from Vietnamese agarwood and its induction effect on brain-derived neurotrophic factor mRNA expression in vitro. Bioorg Med Chem 2006, 14:3571-3574.
• [4]Kumeta Y, Ito M: Characterization of delta-guaiene synthases from cultured cells of Aquilaria, responsible for the formation of the sesquiterpenes in agarwood. Plant Physiol 2010, 154:1998-2007.
• [5]Xu Y, Zhang Z, Wang M, Wei J, Chen H, Gao Z, Sui C, Luo H, Zhang X, Yang Y, Meng H, Li W: Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis. BMC Genomics 2013, 14:227.
• [6]Momma K, Masuzawa Y, Nakai N, Chujo M, Murakami A, Kioka N, Kiyama Y, Akita T, Nagao M: Direct interaction of Cucurbitacin E isolated from Alsomitra macrocarpa to actin filament. Cytotechnology 2008, 56:33-39.
• [7]Chen H, Yang Y, Xue J, Wei J, Zhang Z: 2011. Molecules 2011, 16:4884-4896.
• [8]Chen JC, Chiu MH, Nie RL, Cordell GA, Qiu SX: Cucurbitacins and cucurbitane glycosides: structures and biological activities. Nat Prod Rep 2005, 22:386-399.
• [9]Knecht DA, LaFleur RA, Kahsai AW, Argueta CE, Beshir AB, Fenteany G: Cucurbitacin I inhibits cell motility by indirectly interfering with actin dynamics. PLoS One 2010, 5:e14039.
• [10]Wu PL, Lin FW, Wu TS, Kuoh CS, Lee KH, Lee SJ: Cytotoxic and anti-HIV principles from the rhizomes of Begonia nantoensis. Chem Pharm Bull 2004, 52:345-349.
• [11]Ayyad SE, Abdel-Lateff A, Basaif SA, Shier T: Cucurbitacins-type triterpene with potent activity on mouse embryonic fibroblast from Cucumis prophetarum, cucurbitaceae. Pharmacognosy Res 2011, 3:189-193.
• [12]Ouyang S, Buell CR: The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 2004, 32:D360-D363.
• [13]Ivics Z, Hackett PB, Plasterk RH, Izsvak Z: Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 1997, 91:501-510.
• [14]He ML, Qi SY, Hu LJ: Rapid in vitro propagation of medicinally important Aquilaria agallocha. J Zhejiang Univ Sci B 2005, 6:849-852.
• [15]Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280.
• [16]Song AA, Abdullah JO, Abdullah MP, Shafee N, Othman R, Tan EF, Noor NM, Raha AR: Overexpressing 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) in the lactococcal mevalonate pathway for heterologous plant sesquiterpene production. PLoS One 2012, 7:e52444.
• [17]Benveniste P: Sterol metabolism. Arabidopsis Book 2002, 1:e0004.
• [18]Nakai Y, Nakahira Y, Sumida H, Takebayashi K, Nagasawa Y, Yamasaki K, Akiyama M, Ohme-Takagi M, Fujiwara S, Shiina T, Mitsuda N, Fukusaki E, Kubo Y, Sato MH: Vascular plant one-zinc-finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis. Plant J 2013, 73:761-775.
• [19]Mitsuda N, Hisabori T, Takeyasu K, Sato MH: VOZ; isolation and characterization of novel vascular plant transcription factors with a one-zinc finger from Arabidopsis thaliana. Plant Cell Physiol 2004, 45:845-854.
• [20]Jensen MK, Hagedorn PH, de Torres-Zabala M, Grant MR, Rung JH, Collinge DB, Lyngkjaer MF: Transcriptional regulation by an NAC (NAM-ATAF1,2–CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f. sp. hordei in Arabidopsis. Plant J 2008, 56:867-880.
• [21]Bak S, Beisson F, Bishop G, Hamberger B, Hofer R, Paquette S, Werck-Reichhart D: Cytochromes p450. Arabidopsis Book 2011, 9:e0144.
• [22]Coon MJ: Cytochrome P450: nature’s most versatile biological catalyst. Annu Rev Pharmacol Toxicol 2005, 45:1-25.
• [23]Struck AW, Thompson ML, Wong LS, Micklefield J: S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications. Chembiochem 2012, 13:2642-2655.
• [24]Simpson JT, Durbin R: Efficient de novo assembly of large genomes using compressed data structures. Genome Res 2012, 22:549-556.
• [25]Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W: Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27:578-579.
• [26]Boetzer M, Pirovano W: Toward almost closed genomes with GapFiller. Genome Biol 2012, 13:R56.
• [27]Smit AFA, Hubley R, Green P: Repeatmasker open-3.0. http://www.repeatmasker.org 1996–2010
• [28]Smit AFA, Hubley R: Repeatmodeler open-1.0. http://www.repeatmasker.org 2008–2010
• [29]Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7:562-578.
• [30]Stanke M, Diekhans M, Baertsch R, Haussler D: Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 2008, 24:637-644.
• [31]Zerbino DR, Birney E: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
• [32]Schulz MH, Zerbino DR, Vingron M, Birney E: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28:1086-1092.
• [33]Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD: The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 2005, 33:D284-D288.
• [34]Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
• [35]Roberts A, Pachter L: Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 2013, 10:71-73.
• [36]Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.