Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing

Sago palm (Metroxylon sagu) is an important agricultural starch-producing palm that contributes to Malaysia’s economics, especially in the State of Sarawak. In this palm tree, storage-starch is located in the trunk of the plant. Under normal conditions, the sago palm develops its trunk after 4 - 5 y...

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Main Author:	Wei Jie, Yan
Format:	Thesis
Language:	English English
Published:	2023
Subjects:	Q Science (General) S Agriculture (General)
Online Access:	http://ir.unimas.my/id/eprint/43189/1/Yan%20Wei%20Jie%20%2817010084%29.pdf http://ir.unimas.my/id/eprint/43189/2/Yan%20Wei%20Jie%20%2817010084%29%20Student%20Declaration%20of%20Original%20Work.pdf
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spelling	my-unimas-ir.431892023-10-24T03:00:54Z Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing 2023-11-06 Wei Jie, Yan Q Science (General) S Agriculture (General) Sago palm (Metroxylon sagu) is an important agricultural starch-producing palm that contributes to Malaysia’s economics, especially in the State of Sarawak. In this palm tree, storage-starch is located in the trunk of the plant. Under normal conditions, the sago palm develops its trunk after 4 - 5 years of being planted. However, sago palm planted on deep-peat soil failed to develop their trunk even after 17 years of being planted. This phenomenon is known as ‘non-trunking’, which eliminates the economic value of the palms. Numerous research has been done to address the phenomenon, but the molecular mechanisms of sago palm responding toward the responsible stresses are still lacking. Therefore, this study used the transcriptomic approach to determine differentially expressed enzymes and pathways causing the non-trunking phenomenon. A newly improved CTAB extraction protocol was used for RNA extraction, followed by next-generation transcriptome sequencing using the BGISEQ-500 platform. The sequence was de novo-assembled using TRINITY software package and the differentially expressed genes (DEGs) were identified using DESeq2 algorithm. A total of 40.11 Gb were sequenced from the sago palm leaf samples. The assembled sequence produced 102,447 Unigenes, with an N50 score of 1,809 bp and a GC ratio of 44.34%. The alignment of Unigenes with seven functional databases (NR, NT, GO, KOG, KEGG, SwissProt and InterPro) resulted in the annotation of 65,523 (63.96%) genes. A total of 936 DEGs were identified. Analysis of the DEG data and the pathways involved showed that the non-trunking phenomenon in sago palm is caused by the nutrient deficiency of nitrogen, phosphate and sulphate. The DEG analysis also indicated that nutrient starvation negatively affects the normal biological processes in the sago palm; aggravating the effect of boron and aluminium toxicity; and the malnourished sago palm is also more susceptible to pathogenic infection; which ultimately leads to stunted growth and development of the plant. Unimas Institutional Repository 2023-11 Thesis http://ir.unimas.my/id/eprint/43189/ http://ir.unimas.my/id/eprint/43189/1/Yan%20Wei%20Jie%20%2817010084%29.pdf text en public http://ir.unimas.my/id/eprint/43189/2/Yan%20Wei%20Jie%20%2817010084%29%20Student%20Declaration%20of%20Original%20Work.pdf text en public https://ir.unimas.my/ phd doctoral Universiti Malaysia Sarawak Molecular Biology
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English English
topic	Q Science (General) S Agriculture (General)
spellingShingle	Q Science (General) S Agriculture (General) Wei Jie, Yan Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing
description	Sago palm (Metroxylon sagu) is an important agricultural starch-producing palm that contributes to Malaysia’s economics, especially in the State of Sarawak. In this palm tree, storage-starch is located in the trunk of the plant. Under normal conditions, the sago palm develops its trunk after 4 - 5 years of being planted. However, sago palm planted on deep-peat soil failed to develop their trunk even after 17 years of being planted. This phenomenon is known as ‘non-trunking’, which eliminates the economic value of the palms. Numerous research has been done to address the phenomenon, but the molecular mechanisms of sago palm responding toward the responsible stresses are still lacking. Therefore, this study used the transcriptomic approach to determine differentially expressed enzymes and pathways causing the non-trunking phenomenon. A newly improved CTAB extraction protocol was used for RNA extraction, followed by next-generation transcriptome sequencing using the BGISEQ-500 platform. The sequence was de novo-assembled using TRINITY software package and the differentially expressed genes (DEGs) were identified using DESeq2 algorithm. A total of 40.11 Gb were sequenced from the sago palm leaf samples. The assembled sequence produced 102,447 Unigenes, with an N50 score of 1,809 bp and a GC ratio of 44.34%. The alignment of Unigenes with seven functional databases (NR, NT, GO, KOG, KEGG, SwissProt and InterPro) resulted in the annotation of 65,523 (63.96%) genes. A total of 936 DEGs were identified. Analysis of the DEG data and the pathways involved showed that the non-trunking phenomenon in sago palm is caused by the nutrient deficiency of nitrogen, phosphate and sulphate. The DEG analysis also indicated that nutrient starvation negatively affects the normal biological processes in the sago palm; aggravating the effect of boron and aluminium toxicity; and the malnourished sago palm is also more susceptible to pathogenic infection; which ultimately leads to stunted growth and development of the plant.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Wei Jie, Yan
author_facet	Wei Jie, Yan
author_sort	Wei Jie, Yan
title	Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing
title_short	Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing
title_full	Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing
title_fullStr	Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing
title_full_unstemmed	Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing
title_sort	comparative analysis of gene expressed in trunking and non-trunking metroxylon sagu leaves utilizing transcriptome sequencing
granting_institution	Universiti Malaysia Sarawak
granting_department	Molecular Biology
publishDate	2023
url	http://ir.unimas.my/id/eprint/43189/1/Yan%20Wei%20Jie%20%2817010084%29.pdf http://ir.unimas.my/id/eprint/43189/2/Yan%20Wei%20Jie%20%2817010084%29%20Student%20Declaration%20of%20Original%20Work.pdf
_version_	1783728550533136384

Comparative Analysis of Gene Expressed in Trunking and Non-Trunking Metroxylon sagu Leaves Utilizing Transcriptome Sequencing

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