Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.)
<p>Abstract</p> <p>Background</p> <p>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 <it>in vitro </it>propag...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-10-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/8/381 |
| _version_ | 1811284050695946240 |
|---|---|
| author | Lee Weng-Wah Ooi Siew-Eng Lee Yang-Ping Lim Kok-Ang Ng Wai-Har Tee Sue-Sean Choi Mei-Chooi Kwan Yen-Yen Ho Chai-Ling Tee Jin-Ming Tan Siang-Hee Kulaveerasingam Harikrishna Alwee Sharifah Abdullah Meilina |
| author_facet | Lee Weng-Wah Ooi Siew-Eng Lee Yang-Ping Lim Kok-Ang Ng Wai-Har Tee Sue-Sean Choi Mei-Chooi Kwan Yen-Yen Ho Chai-Ling Tee Jin-Ming Tan Siang-Hee Kulaveerasingam Harikrishna Alwee Sharifah Abdullah Meilina |
| author_sort | Lee Weng-Wah |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>in vitro </it>propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.</p> <p>Results</p> <p>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 <it>CONSTANS</it>-<it>like</it>, <it>AGAMOUS-like (AGL)2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP) </it>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, <it>EgSBP </it>and <it>EgSEP </it>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-13T02:22:48Z |
| format | Article |
| id | doaj.art-29d98ec55b3a48fc9b36c1ed49dc0661 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T02:22:48Z |
| publishDate | 2007-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-29d98ec55b3a48fc9b36c1ed49dc06612022-12-22T03:06:52ZengBMCBMC Genomics1471-21642007-10-018138110.1186/1471-2164-8-381Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.)Lee Weng-WahOoi Siew-EngLee Yang-PingLim Kok-AngNg Wai-HarTee Sue-SeanChoi Mei-ChooiKwan Yen-YenHo Chai-LingTee Jin-MingTan Siang-HeeKulaveerasingam HarikrishnaAlwee SharifahAbdullah Meilina<p>Abstract</p> <p>Background</p> <p>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 <it>in vitro </it>propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.</p> <p>Results</p> <p>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 <it>CONSTANS</it>-<it>like</it>, <it>AGAMOUS-like (AGL)2, AGL20, LFY-like, SQUAMOSA, SQUAMOSA binding protein (SBP) </it>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, <it>EgSBP </it>and <it>EgSEP </it>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/8/381 |
| spellingShingle | Lee Weng-Wah Ooi Siew-Eng Lee Yang-Ping Lim Kok-Ang Ng Wai-Har Tee Sue-Sean Choi Mei-Chooi Kwan Yen-Yen Ho Chai-Ling Tee Jin-Ming Tan Siang-Hee Kulaveerasingam Harikrishna Alwee Sharifah Abdullah Meilina Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.) BMC Genomics |
| title | Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.) |
| title_full | Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.) |
| title_fullStr | Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.) |
| title_full_unstemmed | Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.) |
| title_short | Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (<it>Elaeis guineensis </it>Jacq.) |
| title_sort | analysis and functional annotation of expressed sequence tags ests from multiple tissues of oil palm it elaeis guineensis it jacq |
| url | http://www.biomedcentral.com/1471-2164/8/381 |
| work_keys_str_mv | AT leewengwah analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT ooisieweng analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT leeyangping analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT limkokang analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT ngwaihar analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT teesuesean analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT choimeichooi analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT kwanyenyen analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT hochailing analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT teejinming analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT tansianghee analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT kulaveerasingamharikrishna analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT alweesharifah analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq AT abdullahmeilina analysisandfunctionalannotationofexpressedsequencetagsestsfrommultipletissuesofoilpalmitelaeisguineensisitjacq |