Comparative Transcriptome Reconstruction of Four Hypericum Species Focused on Hypericin Biosynthesis

被引:0
作者
Sotak, Miroslav [1 ]
Czerankova, Odeta [1 ]
Klein, Daniel [2 ]
Jurcackova, Zuzana [1 ]
Li, Ling [3 ,4 ]
Cellarova, Eva [1 ]
机构
[1] Pavol Jozef Safarik Univ, Fac Sci, Inst Biol & Ecol, Dept Genet, Kosice, Slovakia
[2] Pavol Jozef Safarik Univ, Fac Sci, Inst Math, Kosice, Slovakia
[3] Iowa State Univ, Dept Genet Dev & Cell Biol, Ames, IA USA
[4] Iowa State Univ, Ctr Metab Biol, Ames, IA USA
来源
FRONTIERS IN PLANT SCIENCE | 2016年 / 7卷
关键词
Hypericum spp; RNA-Seq; de novo assembly; differential expression analysis; hypericin; ST-JOHNS-WORT; DIFFERENTIAL EXPRESSION; GENUS HYPERICUM; DARK GLANDS; HYP-1; GENE; RNA-SEQ; PERFORATUM;
D O I
10.3389/fpls.2010.01039
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Next generation sequencing technology rapidly developed research applications in the field of plant functional genomics. Several Hypericurn spp. with an aim to generate and enhance gene annotations especially for genes coding the enzymes supposedly included in biosynthesis of valuable bioactive compounds were analyzed. The first de novo transcriptome profiling of Hypericum annulatum Moris, H. tomentosum L. H. kalmianum, and H. androsaemum L. leaves cultivated in vitro was accomplished. All four species with only limited genomic information were selected on the basis of differences in ability to synthesize hypericins and presence of dark nodules accumulating these metabolites with purpose to enrich genomic background of Hypericum spp. H. annulaturn was chosen because of high number of the dark nodules and high content of hypericin. H. tomentosum leaves are typical for the presence of only 1-2 dark nodules localized in the apical part. Both H. kalmianum and H. androsaemum lack hypericin and have no dark nodules. Four separated datasets of the pair-end reads were gathered and used for de novo assembly by Trinity program. Assembled transcriptomes were annotated to the public databases Swiss-Prot and non-redundant protein database (NCBI-nr). Gene ontology analysis was performed. Differences of expression levels in the marginal tissues with dark nodules and inner part of leaves lacking these nodules indicate a potential genetic background for hypericin formation as the presumed site of hypericin biosynthesis is in the cells adjacent to these structures. Altogether 165 contigs in H. annulatum and 100 contigs in H. tomentosum were detected as significantly differentially expressed (P < 0.05) and upregulated in the leaf rim tissues containing the dark nodules. The new sequences homologous to octaketide synthase and enzymes catalyzing phenolic oxidative coupling reactions indispensable for hypericin biosynthesis were discovered. The presented transcriptomic sequence data will improve current knowledge about the selected Hypericum spp. with proposed relation to hypericin biosynthesis and will provide a useful resource of genomic information for consequential studies in the field of functional genomics, proteomics and metabolomics.
引用
收藏
页数:14
相关论文
共 31 条
[1]   Hypericin in cancer treatment: more light on the way [J].
Agostinis, P ;
Vantieghem, A ;
Merlevede, W ;
de Witte, PAM .
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 2002, 34 (03) :221-241
[2]   Differential expression analysis for sequence count data [J].
Anders, Simon ;
Huber, Wolfgang .
GENOME BIOLOGY, 2010, 11 (10)
[3]   Molecular and biochemical characterization of an enzyme responsible for the formation of hypericin in St. John's Wort (Hypericum perforatum L.) [J].
Bais, HP ;
Vepachedu, R ;
Lawrence, CB ;
Stermitz, FR ;
Vivanco, JM .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (34) :32413-32422
[4]   Hypericum in infection: Identification of anti-viral and anti-inflammatory constituents [J].
Birt, Diane F. ;
Widrlechner, Mark P. ;
Hammer, Kimberly D. P. ;
Hillwig, Matthew L. ;
Wei, Jingqiang ;
Kraus, George A. ;
Murphy, Patricia A. ;
McCoy, Joe-Ann ;
Wurtele, Eve S. ;
Neighbors, Jeffrey D. ;
Wiemer, David E. ;
Maury, Wendy J. ;
Price, Jason P. .
PHARMACEUTICAL BIOLOGY, 2009, 47 (08) :774-782
[5]   Conservation Strategies in the Genus Hypericum via Cryogenic Treatment [J].
Brunakova, Katarina ;
Cellarova, Eva .
FRONTIERS IN PLANT SCIENCE, 2016, 7
[6]   Mechanism of action of St John's wort in depression - What is known? [J].
Butterweck, V .
CNS DRUGS, 2003, 17 (08) :539-562
[7]  
Conesa Ana, 2008, Int J Plant Genomics, V2008, P619832, DOI 10.1155/2008/619832
[8]   Structural and functional aspects of PR-10 proteins [J].
Fernandes, Humberto ;
Michalska, Karolina ;
Sikorski, Michal ;
Jaskolski, Mariusz .
FEBS JOURNAL, 2013, 280 (05) :1169-1199
[9]   CD-HIT: accelerated for clustering the next-generation sequencing data [J].
Fu, Limin ;
Niu, Beifang ;
Zhu, Zhengwei ;
Wu, Sitao ;
Li, Weizhong .
BIOINFORMATICS, 2012, 28 (23) :3150-3152
[10]   NUTRIENT REQUIREMENTS OF SUSPENSION CULTURES OF SOYBEAN ROOT CELLS [J].
GAMBORG, OL ;
MILLER, RA ;
OJIMA, K .
EXPERIMENTAL CELL RESEARCH, 1968, 50 (01) :151-+