Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia

Four types of preparation were done prior to de novo sequencing of Ganoderma sp. causing basal stem rot in oil palm located in Sabah, Malaysia. Firstly, at least 12 μg of DNA with the ratio of OD260 to OD2so between 1. 7 and 2.0 was obtained from the mycelia of Ganoerma sp. strain C in order to be s...

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Format:	Thesis
Language:	English English
Published:	2012
Subjects:	SB183-317 Field crops Including cereals forage crops grasses legumes root crops sugar plants textile plants alkaloidal plants medicinal plants
Online Access:	https://eprints.ums.edu.my/id/eprint/38636/1/ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/38636/2/FULLTEXT.pdf
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id	my-ums-ep.38636
record_format	uketd_dc
spelling	my-ums-ep.386362024-05-10T02:52:39Z Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia 2012 SB183-317 Field crops Including cereals, forage crops, grasses, legumes, root crops, sugar plants, textile plants, alkaloidal plants, medicinal plants Four types of preparation were done prior to de novo sequencing of Ganoderma sp. causing basal stem rot in oil palm located in Sabah, Malaysia. Firstly, at least 12 μg of DNA with the ratio of OD260 to OD2so between 1. 7 and 2.0 was obtained from the mycelia of Ganoerma sp. strain C in order to be sent for de novo sequencing. Secondly, the DNA sequencing of PCR amplified region of ITSl, 5.8S rDNA and ITS2 of the four strains of Ganoderma sp. was conducted, revealing that strain A was actually identical to strain E. Both strains were much closely related to strain B than to strain C. Regardless, all the strains were considered to be of the same species when they were compared to the more well-known G. /ucidum. BLAST revealed that the identification of the strains could not be done due to the limited genetic information regarding the species in Genbank database. All of the sequences were submitted to the database and given the accession numbers, therefore freely allowing others to analyze the DNA sequence in the database. The workflow of SOAP, AbySS and Velvet was prepared and tested with the paired-end sequences of human 18 chromosome 12 to compare the contigs produced by them. Unfortunately, no clones containing DNA of Ganoderma sp. were successfully produced. All the preparations were done in anticipation that the assembly and analysis of the de novo sequences of Ganoderma sp. would be hastened. 2012 Thesis https://eprints.ums.edu.my/id/eprint/38636/ https://eprints.ums.edu.my/id/eprint/38636/1/ABSTRACT.pdf text en public https://eprints.ums.edu.my/id/eprint/38636/2/FULLTEXT.pdf text en validuser masters Institut Penyelidikan Bioteknologi Universiti Malaysia Sabah
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	SB183-317 Field crops Including cereals forage crops grasses legumes root crops sugar plants textile plants alkaloidal plants medicinal plants
spellingShingle	SB183-317 Field crops Including cereals forage crops grasses legumes root crops sugar plants textile plants alkaloidal plants medicinal plants Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia
description	Four types of preparation were done prior to de novo sequencing of Ganoderma sp. causing basal stem rot in oil palm located in Sabah, Malaysia. Firstly, at least 12 μg of DNA with the ratio of OD260 to OD2so between 1. 7 and 2.0 was obtained from the mycelia of Ganoerma sp. strain C in order to be sent for de novo sequencing. Secondly, the DNA sequencing of PCR amplified region of ITSl, 5.8S rDNA and ITS2 of the four strains of Ganoderma sp. was conducted, revealing that strain A was actually identical to strain E. Both strains were much closely related to strain B than to strain C. Regardless, all the strains were considered to be of the same species when they were compared to the more well-known G. /ucidum. BLAST revealed that the identification of the strains could not be done due to the limited genetic information regarding the species in Genbank database. All of the sequences were submitted to the database and given the accession numbers, therefore freely allowing others to analyze the DNA sequence in the database. The workflow of SOAP, AbySS and Velvet was prepared and tested with the paired-end sequences of human 18 chromosome 12 to compare the contigs produced by them. Unfortunately, no clones containing DNA of Ganoderma sp. were successfully produced. All the preparations were done in anticipation that the assembly and analysis of the de novo sequences of Ganoderma sp. would be hastened.
format	Thesis
qualification_level	Master's degree
title	Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia
title_short	Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia
title_full	Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia
title_fullStr	Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia
title_full_unstemmed	Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia
title_sort	preparation for de novo sequencing of ganoderma affecting oil palm in sabah, malaysia
granting_institution	Institut Penyelidikan Bioteknologi
granting_department	Universiti Malaysia Sabah
publishDate	2012
url	https://eprints.ums.edu.my/id/eprint/38636/1/ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/38636/2/FULLTEXT.pdf
_version_	1804890331323301888

Preparation for de novo sequencing of ganoderma affecting oil palm in Sabah, Malaysia

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