Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)

Siregar UJ, Maulana MI, Suharsono UW. 2017. Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis). Biodiversitas 18: 1150-1158. Agarwood is one of non timber forest products (NTFP) which has high economic value. Diminishing agarwood trees in natural forest due...

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Autores principales:	ULFAH J. SIREGAR, MUHAMMAD IQBAL MAULANA, UTUT W. SUHARSONO
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2017
Materias:	aquilaria malaccensis blast cloning genomic library Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/fdb81c0d0095433ba396daf9daf686ad
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spelling	oai:doaj.org-article:fdb81c0d0095433ba396daf9daf686ad2021-11-16T13:56:34ZDevelopment of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)1412-033X2085-472210.13057/biodiv/d180336https://doaj.org/article/fdb81c0d0095433ba396daf9daf686ad2017-07-01T00:00:00Zhttps://smujo.id/biodiv/article/view/2035https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Siregar UJ, Maulana MI, Suharsono UW. 2017. Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis). Biodiversitas 18: 1150-1158. Agarwood is one of non timber forest products (NTFP) which has high economic value. Diminishing agarwood trees in natural forest due to intensive harvesting has shifted the production paradigm to forest plantation. In order to support agarwood tree improvement, investigation on the agarwood tree genomes and genes involved in agarwood production is highly needed through genomic library construction. This research aimed at establishing cloning protocols for genomic library construction of agarwood tree (Aquilaria malaccensis) until sequencing process. Genomic DNA was isolated using DNeasy Plant Mini Kit from Qiagen, then was digested with EcoR1, and was ligated to pGemÂ®-T Easy vector system before it was finally transformed and was cloned to E.coli strain DH5Î±. Confirmation of DNA inserts was done using PCR colony with universal primer of SP6 and T7, plasmid isolation and also PCR plasmid and plasmid DNA digestion used Quick Plasmid Miniprep Kit from Thermofisher. Cloned A. malaccensis DNA fragments were sequenced and BLAST at NCBI site. The cloning successfully obtained five white colonies which contain inserted A. malaccensis DNA fragments with the size of 136-225 bp. PCR colony, plasmid isolation, PCR plasmid, and plasmid DNA digestion had confirmed the existence of inserted A. malaccensis DNA genome inside the bacteria cells. Sequencing and BLAST showed that DNA inserts from colony number 6, 8, and 9 were not similar with A. malccensis sequence that was recorded in NCBI, indicating that the genomic region in this library construction is different from the genomic DNA sequences of A. malaccensis in NCBI.ULFAH J. SIREGARMUHAMMAD IQBAL MAULANAUTUT W. SUHARSONOMBI & UNS Soloarticleaquilaria malaccensisblastcloninggenomic libraryBiology (General)QH301-705.5ENBiodiversitas, Vol 18, Iss 3, Pp 1150-1158 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	aquilaria malaccensis blast cloning genomic library Biology (General) QH301-705.5
spellingShingle	aquilaria malaccensis blast cloning genomic library Biology (General) QH301-705.5 ULFAH J. SIREGAR MUHAMMAD IQBAL MAULANA UTUT W. SUHARSONO Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)
description	Siregar UJ, Maulana MI, Suharsono UW. 2017. Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis). Biodiversitas 18: 1150-1158. Agarwood is one of non timber forest products (NTFP) which has high economic value. Diminishing agarwood trees in natural forest due to intensive harvesting has shifted the production paradigm to forest plantation. In order to support agarwood tree improvement, investigation on the agarwood tree genomes and genes involved in agarwood production is highly needed through genomic library construction. This research aimed at establishing cloning protocols for genomic library construction of agarwood tree (Aquilaria malaccensis) until sequencing process. Genomic DNA was isolated using DNeasy Plant Mini Kit from Qiagen, then was digested with EcoR1, and was ligated to pGemÂ®-T Easy vector system before it was finally transformed and was cloned to E.coli strain DH5Î±. Confirmation of DNA inserts was done using PCR colony with universal primer of SP6 and T7, plasmid isolation and also PCR plasmid and plasmid DNA digestion used Quick Plasmid Miniprep Kit from Thermofisher. Cloned A. malaccensis DNA fragments were sequenced and BLAST at NCBI site. The cloning successfully obtained five white colonies which contain inserted A. malaccensis DNA fragments with the size of 136-225 bp. PCR colony, plasmid isolation, PCR plasmid, and plasmid DNA digestion had confirmed the existence of inserted A. malaccensis DNA genome inside the bacteria cells. Sequencing and BLAST showed that DNA inserts from colony number 6, 8, and 9 were not similar with A. malccensis sequence that was recorded in NCBI, indicating that the genomic region in this library construction is different from the genomic DNA sequences of A. malaccensis in NCBI.
format	article
author	ULFAH J. SIREGAR MUHAMMAD IQBAL MAULANA UTUT W. SUHARSONO
author_facet	ULFAH J. SIREGAR MUHAMMAD IQBAL MAULANA UTUT W. SUHARSONO
author_sort	ULFAH J. SIREGAR
title	Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)
title_short	Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)
title_full	Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)
title_fullStr	Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)
title_full_unstemmed	Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)
title_sort	development of protocols for genomic library construction of agarwood (aquilaria malaccensis)
publisher	MBI & UNS Solo
publishDate	2017
url	https://doaj.org/article/fdb81c0d0095433ba396daf9daf686ad
work_keys_str_mv	AT ulfahjsiregar developmentofprotocolsforgenomiclibraryconstructionofagarwoodaquilariamalaccensis AT muhammadiqbalmaulana developmentofprotocolsforgenomiclibraryconstructionofagarwoodaquilariamalaccensis AT ututwsuharsono developmentofprotocolsforgenomiclibraryconstructionofagarwoodaquilariamalaccensis
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Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis)

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