Strategies of the study on Herb Genome Program

Yaoxue Xuebao

Volumn 45, Issue 7, 2010, Pages 807-812

  Chen, Shi Lin ^a   Sun, Yong Zhen ^a   Xu, Jiang ^a   Luo, Hong Mei ^a   Sun, Chao ^a   He, Liu ^a   Cheng, Xiang Lin ^b   Zhang, Bo Li ^c   Xiao, Pei Gen ^a  

^a INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

^b China National Center for Biotechnology Development   (China)

^c TIANJIN UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

Author keywords

Herb Genome Program; Medicinal plants; Post genomics; Secondary metabolism; Whole genome sequencing

Indexed keywords

BIOINFORMATICS; CHINESE MEDICINE; GENE SEQUENCE; GENOME; HERB; MEDICINAL PLANT; REVIEW; TRADITIONAL MEDICINE;

CHINA; CHROMOSOME MAPPING; GENOME, PLANT; GENOMICS; MEDICINE, CHINESE TRADITIONAL; METABOLIC NETWORKS AND PATHWAYS; MUTATION; PLANTS, MEDICINAL; SEQUENCE ANALYSIS, DNA;

EID: 77956463809     PISSN: 05134870     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (42)

1. Chinese Medicinal Corporation. Chinese Traditional Medicine Resource Records [M]. Beijing: Science Press, 1995.
2. Graham IA, Besser K, Blumer S, et al. The genetic map of Artemisia annua L. identifies loci affecting yield of the anti-malarial drug artemisinin [J]. Science, 2010, 327: 328-331.
3. Li Y, Sun C, Luo HM, et al. Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX [J]. Acta Pharm Sin, 2010, 45: 524-529.
4. Sun C, Li Y, Wu Q, et al. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis [J]. BMC Genomics, 2010, 11: 262.
5. Li Y, Luo HM, Sun C, et al. EST analysis reveals putative genes involved in glycyrrhizin biosynthesis [J]. BMC Genomics, 2010, 11: 268.
6. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J]. Nature, 2000, 408: 796-815.
7. International Rice Genome Sequencing Project. The map-based sequence of the rice genome [J]. Nature, 2005, 436: 793-800.
8. Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) [J]. Science, 2002, 296: 92-100. (Pubitemid 34280065)
9. Yu J, Hu SN, Wang J, et al. A draft Sequence of the rice genome (Oryza sativa L. ssp. indica) [J]. Science, 2002, 296: 79-92.
10. Tuskan GA, Difazio D, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) [J]. Science, 2006, 313: 1596-1604.
11. Rensing SA, Lang D, Zimmer AD, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants [J]. Science, 2008, 319: 64-69.
12. Schnable PS, Ware D, Fulton RS, et al. The B73 maize genome: complexity, diversity, and dynamics [J]. Science, 2009, 326: 1112-1115.
13. Jaillon O, Aury JM, Noel B, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla [J]. Nature, 2007, 449: 463-467.
14. Ming R, Hou SB, Feng Y, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) [J]. Nature, 2008, 452: 991-996.
15. Paterson AH, Bowers JE, Bruggmann R, et al. The Sorghum bicolor genome and the diversification of grasses [J]. Nature, 2009, 457: 551-556.
16. Huang SW, Li RQ, Zhang ZH, et al. The genome of the cucumber (Cucumis sativus L) [J]. Nat Genet, 2009, 41: 1275-1281.
17. Schmutz J, Cannon SB, Schlueter J, et al. Genome sequence of the palaeopolyploid soybean [J]. Nature, 2010, 463: 178-183.
18. The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon [J]. Nature, 2010, 463: 763-768.
19. Edwards D, Batley J. Plant genome sequencing: applications for crop improvement [J]. Plant Biotechnol J, 2009, 8: 2-9.
20. Wang QH, Chen AH, Zhang BL. Salviae Miltiorrhiza: a model organism for Chinese Traditional Medicine genomic studies [J]. Acta Chin Med Pharm, 2009, 37: 1-3.
21. Chen SL, Yao H, Han JP, et al. Validation of the ITS2 Region as a novel DNA barcode for identifying medicinal plant species [J]. PLoS One, 2010, 5: e8613.
22. Pang XH, Song JY, Zhu YJ, et al. Applying plant DNA barcodes for Rosaceae species identification [J]. Cladistics, 2010, 26: 1-6.
23. Van Duren M, Morpurgo R, Dolezel J, et al. Induction and verification of autotetraploids and diploid banana (Musa acuminata) by in vitro techniques [J]. Euphytica, 1996, 88: 25-34. (Pubitemid 3036310)
24. Dolezel J, Greilhuber J, Suda J. Estimation of nuclear DNA content in plants using flow cytometry [J]. Nat Protoc, 2007, 2: 2233-2244. (Pubitemid 351565863)
25. Metzker ML. Sequencing technologies - the next generation [J]. Nat Rev Genet, 2010, 11: 31-46.
26. Illumina. http://www.illumina.com/systems/hiseq-2000.ilmn [OL].
27. De Schutter K, Lin YC, Tiels P, et al. Genome sequence of the recombinant protein production host Pichia pastoris [J]. Nat biotechnol, 2009, 27: 561-566.
28. Vu GT, Dear PH, Caligari PD, et al. BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping [J]. PLoS One, 2010, 5: e9089.
29. Hamilton EP, Dear PH, Rowland T, et al. Use of Happy mapping for the higher order assembly of the Tetrahymena genome [J]. Genomics, 2006, 88: 443-451. (Pubitemid 44397447)
30. Latreille P, Norton S, Goldman BS, et al. Optical mapping as a routine tool for bacterial genome sequence finishing [J]. BMC Genomics, 2007, 8: 321. (Pubitemid 350020808)
31. Imelfort M, Edwards D. De novo sequencing plant genomes using second-generation technologies [J]. Brief bioinform, 2009, 10: 609-618.
32. Lynn AM, Jain CK, Kosalai K, et al. An automated annotation tool for genomic DNA sequences using GeneScan and BLAST [J]. J Genet, 2001, 80: 9-16. (Pubitemid 33576379)
33. Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA [J]. Genome Res, 2000, 10: 516-522.
34. Zdobnov EM, Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro [J]. Bioinformatics, 2001, 53: 847-848. (Pubitemid 32970486)
35. Joslyn CA, Mniszewski SM, Fulmer A, et al. The gene ontology categorizer [J]. Bioinformatics, 2004, 20: 169-177.
36. Kanehisa M, Goto S, Hattori M, et al. From genomics to chemical genomics: new developments in KEGG [J]. Nucleic Acids Res, 2006, 34: 354-357.
37. McCallum CM, Comai L, Greene EA, et al. Targeted screening for induced mutations [J]. Nat Biotechnol, 2000, 18: 455-457.
38. Sessions A, Burke E, Presting G, et al. A high-throughput Arabidopsis reverse genetics system [J]. Plant Cell, 2002, 14: 2985-2994.
39. Sallaud C, Gay C, Larmande P, et al. High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics [J]. Plant J, 2004, 39: 450-464.
40. van der Fits L, Memelink J. ORCA3, a jasmonate-responsive transcriptional regulator of plant primary and secondary metabolism [J]. Science, 2000, 289: 295-297.
41. Collu G, Unver N, Peltenburg-Looman AMG, et al. Geraniol 10-hydroxylase1, a cytochrome P450 enzyme involved in terpenoid indole alkaloid biosynthesis [J]. FEBS Lett, 2001, 508: 215-220.
42. Seki H, Ohyama K, Sawai S, et al. Licorice β-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin [J]. Proc Natl Acad Sci USA, 2008, 105: 14204-14209.