Transcriptome analyses of a Chinese hazelnut species Corylus mandshurica

BMC Plant Biology

Volumn 13, Issue 1, 2013, Pages

  Ma, Hui ^a   Lu, Zhiqiang ^a   Liu, Bingbing ^a   Qiu, Qiang ^a   Liu, Jianquan ^a  

^a LANZHOU UNIVERSITY   (China)

Author keywords

Adaptation; Cold frigid; Corylus mandshurica; Divergence; Fungi fungus; Taxol paclitaxel; Transcriptome

Indexed keywords

CORYLUS; CORYLUS AVELLANA; CORYLUS COLURNA CHINENSIS; CORYLUS MANDSHURICA; MAGNOLIOPHYTA;

PACLITAXEL; TRANSCRIPTOME;

ARTICLE; GENE EXPRESSION REGULATION; GENETICS; HAZELNUT; METABOLISM;

CORYLUS; GENE EXPRESSION REGULATION, PLANT; PACLITAXEL; TRANSCRIPTOME;

EID: 84884930876     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-13-152     Document Type: Article

References (52)

1. Zhang Y, Li F, Tao R, Li Z, Liang Y. An investigation of wild Corylus resource at Changbai Mountains. J Jilin Agri Sci 2007, 32(5):56-57.
2. Liu H. Exploring the utilization of Corylus. Farm Prod Proc 2010, 1:24-25.
3. Huang M. Selecting for excellent clones of Castanea henryi. Fujian Agri Sci Technol 2012, 12:35-40.
4. Liu Y, Zhang H, Zhang W. The new application of Corylus. Spel Econ Anim Plant 1998, 6:38.
5. Plosker GL, Hurst M. Paclitaxel: a pharmacoeconomic review of its use in non-small cell lung cancer. Pharmacoeconomics 2001, 19(11):1111-1134. 10.2165/00019053-200119110-00005, 11735678.
6. Kumar S, Mahdi H, Bryant C, Shah JP, Garg G, Munkarah A. Clinical trials and progress with paclitaxel in ovarian cancer. Inter J Women's Health 2010, 2:411-427.
7. Gradishar WJ. Taxanes for the treatment of metastatic breast cancer. Bre Can: Basic Clin Res 2012, 6:159-171.
8. Wani MC, Taylor HL, Wall ME, Coggon P, McPhail AT. Plant antitumor agents. VI. Isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. J Am Chem Soc 1971, 93(9):2325-2327. 10.1021/ja00738a045, 5553076.
9. Vidensek N, Lim P, Campbell A, Carlson C. Taxol content in bark, wood, root, leaf, twig, and seedling from several Taxus species. J Nat Prod 1990, 53(6):1609-1610. 10.1021/np50072a039, 1982448.
10. Service RF. Hazel trees offer new source of cancer drug. Science 2000, 288(5463):27-28.
11. Bestoso F, Ottaggio L, Armirotti A, Balbi A, Damonte G, Degan P, Mazzei M, Cavalli F, Ledda B, Miele M. In vitro cell cultures obtained from different explants of Corylus avellana produce Taxol and taxanes. BMC Biotechnol 2006, 6(1):45. 10.1186/1472-6750-6-45, 1702537, 17150090.
12. Hoffman A, Shahidi F. Paclitaxel and other taxanes in hazelnut. J Funct Foods 2009, 1(1):33-37.
13. Ottaggio L, Bestoso F, Armirotti A, Balbi A, Damonte G, Mazzei M, Sancandi M, Miele M. Taxanes from Shells and Leaves of Corylus avellana. J Nat Prod 2007, 71(1):58-60.
14. Luo F, Fei X, Tang F, Li X. Simultaneous determination of Paclitaxel in hazelnut by HPLC-MS/MS. For Res 2011, 24(6):779-783.
15. Miele M, Mumot A, Zappa A, Romano P, Ottaggio L. Hazel and other sources of paclitaxel and related compounds. Phytochem Rev 2012, 11(2-3):211-225.
16. Liu X-K, Liu J-J. New source for L-iditol and taxanes. Nat Preced 2008, , http://precedings.nature.com/documents/1502/version/1
17. Bemani E, Ghanati F, Rezaei A, Jamshidi M. Effect of phenylalanine on taxol production and antioxidant activity of extracts of suspension-cultured hazel (Corylus avellana L.) cells. J Nat Med 2013, 67(3):446-451. 10.1007/s11418-012-0696-1, 22847380.
18. Zhao D, Su S, Ni B, Wang W, Meng X, Liu W. Germplasm resources investigation and utilization prospects of hazel in Small Xing'an Ridge region. Chin Agric Sci Bull 2012, 28(28):87-94.
19. Coyne CJ, Mehlenbacher SA, Smith DC. Sources of resistance to Eastern Filbert Blight in hazelnut. J Am Soc Hortic Sci 1998, 123(2):253-257.
20. Molnar TJ, Capik J, Zhao S, Zhang N. First report of Eastern Filbert Blight on Corylus avellana 'Gasaway' and 'VR20-11' caused by Anisogramma anomala in New Jersey. Plant Dis 2010, 94(10):1265-1265.
21. Liang W. An investigation of wild Corylus resources in China. Journal of Liaoning Forestry Science and Technology 1989, 1:45-52.
22. Peng L, Wang M, Liang W, Xie M, Li D. A study on cold resistance for filbert genus (Corylus L.) plants. J Jilin Fores Univ 1994, 3:166-170.
23. Ni B, Ni W, Xu X, Wang X. Hazel breeding research. Forest By-Product and Speciality in China 2010, 106(3):29-31.
24. X-j Z, F-x D, R-q Z, G-x W, M-p Y, L-s L. Research on the compatibility of five Corylus species. J Cen South Univ Fores Technol 2009, 29(4):26-30.
25. Erdogan V, Mehlenbacher SA. Interspecific hybridization in hazelnut (Corylus). J Am Soc Hortic Sci 2000, 125(4):489-497.
26. Liang W, Xie M, Dong D, Jiang Z. The breeding research for new Corylus cultivar. China Fruits 2000, 2:4-6.
27. Cheng L, Huang W, Zhou Z, Liu J, Wang Y, Su S, Zhai M. Genetic diversity of six Corylus species in China detected with microsatellite isolated from Corylus avellana. Scientia Silvae Sinicae 2009, 45(2):22-26.
28. Li X, Li X, Wang Z, Xue C, Limin Z, Guo Y. Study on phylogenetic analysis of Corylus germplasm resouces with SSR molecular markers for Corylus avellana. J Northeast Agric Univ 2011, 42(4):129-136.
29. Rowley ER, Fox SE, Bryant DW, Sullivan CM, Priest HD, Givan SA, Mehlenbacher SA, Mockler TC. Assembly and characterization of the European hazelnut 'Jefferson' transcriptome. Crop Sci 2012, 52(6):2679-2686.
30. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652. 10.1038/nbt.1883, 3571712, 21572440.
31. Min XJ, Butler G, Storms R, Tsang A. OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 2005, 33(suppl 2):W677-W680. 1160155, 15980561.
32. Wang N, Thomson M, Bodles WJA, Crawford RMM, Hunt HV, Featherstone AW, Pellicer J, Buggs RJA. Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol 2013, 22(11):3098-3111. 10.1111/mec.12131, 23167599.
33. Kent WJ. BLAT-The BLAST-Like Alignment Tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
34. Altschul SF, Madden TL, Schäffer 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(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
35. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676. 10.1093/bioinformatics/bti610, 16081474.
36. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35(suppl 2):W182-W185. 1933193, 17526522.
37. Srivastava A, Cai L, Mrázek J, Malmberg RL. Mutational patterns in RNA secondary structure evolution examined in three RNA families. PLoS ONE 2011, 6(6):e20484. 10.1371/journal.pone.0020484, 3117835, 21698102.
38. Pelletier J, Sonenberg N. Insertion mutagenesis to increase secondary structure within the 5' noncoding region of a eukaryotic mRNA reduces translational efficiency. Cell 1985, 40(3):515-526. 10.1016/0092-8674(85)90200-4, 2982496.
39. Brown PH, Tiley LS, Cullen BR. Effect of RNA secondary structure on polyadenylation site selection. Genes Dev 1991, 5(7):1277-1284. 10.1101/gad.5.7.1277, 1712333.
40. McManus CJ, Graveley BR. RNA structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 2011, 21(4):373-379. 10.1016/j.gde.2011.04.001, 3149766, 21530232.
41. Mauger DM, Siegfried NA, Weeks KM. The genetic code as expressed through relationships between mRNA structure and protein function. FEBS Lett 2013, 587(8):1180-1188. 10.1016/j.febslet.2013.03.002, 23499436.
42. Amini F, Ismail E. 3′-UTR variations and G6PD deficiency. J Hum Genet 2013, 58(4):189-194. 10.1038/jhg.2012.155, 23389243.
43. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 2006, 34(suppl 2):W293-W297. 1538768, 16845012.
44. Xiong Z, Yang Y, Zhao N, Wang Y. Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglojap yew. Taxus x media. BMC Microbiol 2013, 13(1):71. 10.1186/1471-2180-13-71, 3618195, 23537181.
45. Li S, Zhang P, Zhang M, Fu C, Yu L. Functional analysis of a WRKY transcription factor involved in transcriptional activation of the DBAT gene in Taxus chinensis. Plant Biol 2013, 15(1):19-26. 10.1111/j.1438-8677.2012.00611.x, 22686366.
46. Nims E, Vongpaseuth K, Roberts SC, Walker EL. WITHDRAWN: TcJAMYC: A bHLH transcription factor that activates paclitaxel biosynthetic pathway genes in yew (This manuscript was accepted by the Journal of Biological Chemistry, but following acceptance discrepancies in some of the sequences used in the work were discovered. The manuscript was withdrawn, and additional work has been conducted. Submission of a new manuscript is anticipated.). J Biol Chem 2009, , http://www.jbc.org/content/early/2009/10/01/jbc.M109.026195
47. Sun G, Yang Y, Xie F, Wen J-F, Wu J, Wilson IW, Tang Q, Liu H, Qiu D. Deep sequencing reveals transcriptome re-programming of Taxus × media cells to the elicitation with methyl jasmonate. PLoS ONE 2013, 8(4):e62865. 10.1371/journal.pone.0062865, 3639896, 23646152.
48. Chen F, Tholl D, Bohlmann J, Pichersky E. The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom. Plant J 2011, 66(1):212-229. 10.1111/j.1365-313X.2011.04520.x, 21443633.
49. Guo BH, Wang YC, Hu H, Miao ZQ, Tang KX. An endophytic Taxol-producing fungus BT2 isolated from Taxus chinensis var. maire. Afr J Biotechnol 2006, 5(10):875-877.
50. Zhang P, Zhou P-P, Yu L-J. An endophytic taxol-producing fungus from Taxus media, Cladosporium cladosporioides MD2. Curr Microbiol 2009, 59(3):227-232. 10.1007/s00284-008-9270-1, 19484305.
51. Wei Y, Zhou X, Liu L, Lu J, Wang Z, Yu G, Hu L, Lin J, Sun X, Tang K. An efficient transformation system of taxol-producing endophytic fungus EFY-21 (Ozonium sp.). Afr J Biotechnol 2010, 9(12):1726-1733.
52. Qiu Q, Ma T, Hu Q, Liu B, Wu Y, Zhou H, Wang Q, Wang J, Liu J. Genome-scale transcriptome analysis of the desert poplar. Populus euphratica. Tree Physiol 2011, 31(4):452-461. 10.1093/treephys/tpr015, 21427158.