Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach
White kelampayan (Neolamarckia cadamba) is an indigenous tree species under Rubiaceae family. It has a high economic value due to its fast growing properties. However, an understanding on genetics study of kelampayan still remains scarce. Objectives of this study were to define functional annotati...
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| Format: | Final Year Project Report / IMRAD |
| Language: | English English |
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Universiti Malaysia Sarawak, (UNIMAS)
2015
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/10847/ http://ir.unimas.my/id/eprint/10847/1/Lim.pdf http://ir.unimas.my/id/eprint/10847/4/Lim%20Leong%20ft.pdf |
| _version_ | 1848836872965455872 |
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| author | Lim, Leong Rui |
| author_facet | Lim, Leong Rui |
| author_sort | Lim, Leong Rui |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | White kelampayan (Neolamarckia cadamba) is an indigenous tree species under Rubiaceae family. It has a
high economic value due to its fast growing properties. However, an understanding on genetics study of
kelampayan still remains scarce. Objectives of this study were to define functional annotation and analyse
transcripts expression level of the RNA-Seq data from the white kelampayan. In this study, there were 66,468
transcripts expressed via sequence reads assembly. Out of the total expressed transcripts, 29,495 transcripts
were annotated and mapped with the gene ontology (GO) terms by using bioinformatics approaches such as
the CLC Genomics Workbench 7.5, Blast2GO® and WEGO tool. Differential expression of transcripts was
studied and certain candidate genes involving in wood formation, stress response and plant defence were
identified. In this study, out of 66,468 transcripts, the number of up-regulated transcripts was higher than the
number of down-regulated transcripts, showing more transcripts expressed in the developing xylem tissues.
In gene ontology analysis, the biological processes showed the highest distribution of annotated transcripts.
Besides, cinnamoyl-dehydrogenase, cinnamoyl 4-hydroxylase, cellulose synthase, enzyme antioxidant, heat
shock protein, aquaporin, and genes involved in plant defense were annotated and discussed in this study.
This study provides another useful genomic reference for future research on the tree species. |
| first_indexed | 2025-11-15T06:30:40Z |
| format | Final Year Project Report / IMRAD |
| id | unimas-10847 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English English |
| last_indexed | 2025-11-15T06:30:40Z |
| publishDate | 2015 |
| publisher | Universiti Malaysia Sarawak, (UNIMAS) |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-108472024-02-20T07:53:36Z http://ir.unimas.my/id/eprint/10847/ Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach Lim, Leong Rui SB Plant culture White kelampayan (Neolamarckia cadamba) is an indigenous tree species under Rubiaceae family. It has a high economic value due to its fast growing properties. However, an understanding on genetics study of kelampayan still remains scarce. Objectives of this study were to define functional annotation and analyse transcripts expression level of the RNA-Seq data from the white kelampayan. In this study, there were 66,468 transcripts expressed via sequence reads assembly. Out of the total expressed transcripts, 29,495 transcripts were annotated and mapped with the gene ontology (GO) terms by using bioinformatics approaches such as the CLC Genomics Workbench 7.5, Blast2GO® and WEGO tool. Differential expression of transcripts was studied and certain candidate genes involving in wood formation, stress response and plant defence were identified. In this study, out of 66,468 transcripts, the number of up-regulated transcripts was higher than the number of down-regulated transcripts, showing more transcripts expressed in the developing xylem tissues. In gene ontology analysis, the biological processes showed the highest distribution of annotated transcripts. Besides, cinnamoyl-dehydrogenase, cinnamoyl 4-hydroxylase, cellulose synthase, enzyme antioxidant, heat shock protein, aquaporin, and genes involved in plant defense were annotated and discussed in this study. This study provides another useful genomic reference for future research on the tree species. Universiti Malaysia Sarawak, (UNIMAS) 2015 Final Year Project Report / IMRAD NonPeerReviewed text en http://ir.unimas.my/id/eprint/10847/1/Lim.pdf text en http://ir.unimas.my/id/eprint/10847/4/Lim%20Leong%20ft.pdf Lim, Leong Rui (2015) Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach. [Final Year Project Report / IMRAD] (Unpublished) |
| spellingShingle | SB Plant culture Lim, Leong Rui Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach |
| title | Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach |
| title_full | Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach |
| title_fullStr | Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach |
| title_full_unstemmed | Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach |
| title_short | Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach |
| title_sort | functional annotation and transcript expression analysis of rna-seq data (via ngs) from white kelampayan (neolamarckia cadamba) using bioinformatics approach |
| topic | SB Plant culture |
| url | http://ir.unimas.my/id/eprint/10847/ http://ir.unimas.my/id/eprint/10847/1/Lim.pdf http://ir.unimas.my/id/eprint/10847/4/Lim%20Leong%20ft.pdf |