Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.)
详细信息 查看全文
- 作者：Chai-Ling Ho (1)
Yen-Yen Kwan (1) (9)
Mei-Chooi Choi (1) (7)
Sue-Sean Tee (1)
Wai-Har Ng (1) (11)
Kok-Ang Lim (1)
Yang-Ping Lee (1) (10)
Siew-Eng Ooi (2)
Weng-Wah Lee (1) (3)
Jin-Ming Tee (1) (8)
Siang-Hee Tan (1) (4)
Harikrishna Kulaveerasingam (1) (5)
Sharifah Shahrul Rabiah Syed Alwee (2) (6)
Meilina Ong Abdullah (2) - 刊名：BMC Genomics
- 出版年：2007
- 出版时间：December 2007
- 年：2007
- 卷：8
- 期：1
- 全文大小：850KB
- 参考文献：1. Corley RHV, Tinker PB: / The Oil Palm / 4 Edition UK: Blackwell publishing 2003. CrossRef
2. Corley RHV, Lee CH, Law LH, Wong CY: Abnormal development in oil palm clones. / The Planter 1986, 62:233鈥?40.
3. Flood J, Keenan L, Wayne S, Hasan Y: Studies on oil palm trunks as sources of infection in the field. / Mycopathologia 2005, 159:101鈥?07. CrossRef
4. Ariffin D, Idris AS, Gurmit S: Status of Ganoderma in oil palm. / Ganoderma diseases of perennial crops / (Edited by: Flood J, Bridge PD, Holderness M). UK: CABI Publishing 2000, 49鈥?8. CrossRef
5. Jouannic S, Argout X, Lechauve F, Fizames C, Borgel A, Morcillo F, Aberlenc-Bertossi F, Duval Y, Tregear J: Analysis of expressed sequence tags from oil palm ( Elaeis guineensis ). / FEBS Lett 2005, 579:2709鈥?714. CrossRef
6. Stekel DJ, Git Y, Falciani F: The comparison of gene expression from multiple cDNA libraries. / Genome Res 2000, 10:2055鈥?061. CrossRef
7. Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF: B and C floral organ identity functions require SEPALLATA MADS-box genes. / Nature 2000, 405:200鈥?03. CrossRef
8. Zaidah R: The analysis of the tissue specific loacalization patterns of expression of several oil palm genes during floral development. / MSc thesis Universiti Putra Malaysia 2001.
9. Adam H, Jouannic S, Morcillo F, Richaud F, Duval Y, Tregear JW: MADS box genes in oil palm ( Elaeis guineensis ): Patterns in the evolution of the SQUAMOSA, DEFICIENS, GLOBOSA, AGAMOUS , and SEPALLATA subfamilies. / J Mol Evol 2006, 62:15鈥?1. CrossRef
10. Klein J, Saedler H, Huijser P: A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA . / Mol Gen Genet 1996, 250:7鈥?6.
11. Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, Huijser P: Molecular characterization of the Arabidopsis SBP-box genes. / Gene 1999, 237:91鈥?04. CrossRef
12. Fowler S, Lee K, Onouchi H, Samach A, Richardson K, Morris B, Coupland G, Putterill J: GIGANTEA : a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. / EMBO J 1999, 18:4679鈥?688. CrossRef
13. Rochester DE, Winter JA, Shah DM: The structure and expression of maize genes encoding the major heat shock protein, hsp70. / EMBO J 1986, 5:451鈥?58.
14. Schultz DJ, Craig R, Cox-Foster DL, Mumma RO, Medford JI: RNA isolation from recalcitrant plant tissue. / Plant Mol Biol Reptr 1994, 12:310鈥?16. CrossRef
15. Gli拧in V, Crkvenjakov R, Byus C: Ribonucleic acid isolation by cesium chloride centrifugation. / Biochemistry 1974, 13:2633鈥?637. CrossRef
16. Sambrook J, Fritisch EF, Maniatis T: / Molecular Cloning: A Laboratory Manual / 2 Edition New York: Cold Spring Harbor Laboratory Press 1989.
17. Ewing B, Hillier L, Wendhl MC, Green P: Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. / Genome Res 1998, 8:175鈥?85.
18. Chou H, Holmes MH: DNA sequence quality trimming and vector removal. / Bioinformatics 2001, 17:1093鈥?104. CrossRef
19. Huang X, Madan A: CAP3: A DNA sequence assembly program. / Genome Res 1999, 9:868鈥?77. CrossRef
20. Altschul SF, Madden TL, Schaffer AA, Zhang I, 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鈥?402. CrossRef
21. Blast2Go [http://www.Blast2GO.de]
22. Conesa A, G枚tz S, Garc铆a-G贸mez JM, Terol J, Tal贸n M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. / Bioinformatics 2005, 21:3674鈥?676. CrossRef
23. IDEG6 [hon.bio.unipd.it/bioinfo/IDEG6_form" class="a-plus-plus">http://telethon.bio.unipd.it/bioinfo/IDEG6_form]
24. Romualdi C, Bortoluzzi S, d'Alessi F, Danieli GA: IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. / Physiol Genomics 2003, 12:159鈥?62. - 作者单位：Chai-Ling Ho (1)
Yen-Yen Kwan (1) (9)
Mei-Chooi Choi (1) (7)
Sue-Sean Tee (1)
Wai-Har Ng (1) (11)
Kok-Ang Lim (1)
Yang-Ping Lee (1) (10)
Siew-Eng Ooi (2)
Weng-Wah Lee (1) (3)
Jin-Ming Tee (1) (8)
Siang-Hee Tan (1) (4)
Harikrishna Kulaveerasingam (1) (5)
Sharifah Shahrul Rabiah Syed Alwee (2) (6)
Meilina Ong Abdullah (2)
1. Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM-Serdang, Selangor, Malaysia
9. Institut fur Genetics, University zu Koln, Zulpicherstr. 47, 50674, Koln, Germany
7. Interscience Sdn Bhd. 26 & 28, Jalan 25/34 Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia
11. Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre of Singapore, 11, Hospital Drive, 169610, Singapore
10. Friedrich Miescher Institute, Maulbeerstrasse 66, 4058, Basel, CH, Switzerland
2. Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6 Persiaran Institusi, Bandar Baru Bangi, Selangor, Malaysia
3. KOOPrime Technologies (M) Sdn Bhd, 729, Block B, Jalan PJS 8/5, Mentari Business Park, Dataran Mentari, 46150, Petaling Jaya, Selangor, Malaysia
8. Hubrecht Institute, Uppsalalaan 8, 3584, Utrecht, CT, The Netherlands
4. Sime Plantations Sdn. Bhd., Wisma CONSPLANT 1, 2, Jalan SS 16/4, 47500, Subang Jaya, Selangor, Malaysia
5. Sime Darby Technology Centre Sdn. Bhd., 2, Jalan Tandang, 46050, Petaling Jaya, Selangor, Malaysia
6. Felda Agricultural Services Sdn Bhd., 7th Floor, Balai Felda, Jalan Gurney 1, 54000, Kuala Lumpur, Malaysia
文摘
Background Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm. Results In this study, six cDNA libraries from oil palm zygotic embryos, suspension cells, shoot apical meristems, young flowers, mature flowers and roots, were constructed. We have generated a total of 14537 expressed sequence tags (ESTs) from these libraries, from which 6464 tentative unique contigs (TUCs) and 2129 singletons were obtained. Approximately 6008 of these tentative unique genes (TUGs) have significant matches to the non-redundant protein database, from which 2361 were assigned to one or more Gene Ontology categories. Predominant transcripts and differentially expressed genes were identified in multiple oil palm tissues. Homologues of genes involved in many aspects of flower development were also identified among the EST collection, such as CONSTANS-like, AGAMOUS-like (AGL)2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP) etc. Majority of them are the first representatives in oil palm, providing opportunities to explore the cause of epigenetic homeotic flowering abnormality in oil palm, given the importance of flowering in fruit production. The transcript levels of two flowering-related genes, EgSBP and EgSEP were analysed in the flower tissues of various developmental stages. Gene homologues for enzymes involved in oil biosynthesis, utilization of nitrogen sources, and scavenging of oxygen radicals, were also uncovered among the oil palm ESTs. Conclusion The EST sequences generated will allow comparative genomic studies between oil palm and other monocotyledonous and dicotyledonous plants, development of gene-targeted markers for the reference genetic map, design and fabrication of DNA array for future studies of oil palm. The outcomes of such studies will contribute to oil palm improvements through the establishment of breeding program using marker-assisted selection, development of diagnostic assays using gene targeted markers, and discovery of candidate genes related to important agronomic traits of oil palm.