Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome

Metagenomic DNA library from palm oil mill effluent (POME) was constructed and subjected to high-throughput screening to find genes encoding cellulose- and xylan-degrading enzymes. DNA of 30 positive fosmid clones were sequenced with next generation sequencing technology and the raw data (short inse...

Full description

Bibliographic Details
Main Authors:	Benbelgacem, Farah Fadwa, Mohd Noor Mat Isa, Abdelrahim, Muhammad Alfatih Muddathir, Afidalina Tumian, Bellag, Oualid Abdelkader, Adibah Parman, Ibrahim Ali Noorbatcha, Hamzah Mohd Salleh
Format:	Article
Language:	English
Published:	Penerbit Universiti Kebangsaan Malaysia 2018
Online Access:	http://journalarticle.ukm.my/12915/ http://journalarticle.ukm.my/12915/ http://journalarticle.ukm.my/12915/1/03%20Farah%20Fadwa%20Benbelgacem.pdf

id	ukm-12915
recordtype	eprints
spelling	ukm-129152019-05-15T10:57:16Z http://journalarticle.ukm.my/12915/ Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome Benbelgacem, Farah Fadwa Mohd Noor Mat Isa, Abdelrahim, Muhammad Alfatih Muddathir Afidalina Tumian, Bellag, Oualid Abdelkader Adibah Parman, Ibrahim Ali Noorbatcha, Hamzah Mohd Salleh, Metagenomic DNA library from palm oil mill effluent (POME) was constructed and subjected to high-throughput screening to find genes encoding cellulose- and xylan-degrading enzymes. DNA of 30 positive fosmid clones were sequenced with next generation sequencing technology and the raw data (short insert-paired) was analyzed with bioinformatic tools. First, the quality of 64,821,599 reverse and forward sequences of 101 bp length raw data was tested using Fastqc and SOLEXA. Then, raw data filtering was carried out by trimming low quality values and short reads and the vector sequences were removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained. The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de Bruijn graph algorithm. Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE, where 2139 scaffolds have been reconstructed. 16,386 genes have been identified after gene prediction using Prodigal and putative ID assignment with Blastp vs NR protein. The acceptable strategy to handle metagenomic NGS-data in order to detect known and potentially unknown genes is presented and we showed the computational efficiency of de Bruijn graph algorithm of de novo assembly to 21 bioprospect genes encoding cellulose-degrading enzymes and 6 genes encoding xylan-degrading enzymes of 30.3% to 100% identity percentage. Penerbit Universiti Kebangsaan Malaysia 2018-12 Article PeerReviewed application/pdf en http://journalarticle.ukm.my/12915/1/03%20Farah%20Fadwa%20Benbelgacem.pdf Benbelgacem, Farah Fadwa and Mohd Noor Mat Isa, and Abdelrahim, Muhammad Alfatih Muddathir and Afidalina Tumian, and Bellag, Oualid Abdelkader and Adibah Parman, and Ibrahim Ali Noorbatcha, and Hamzah Mohd Salleh, (2018) Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome. Sains Malaysiana, 47 (12). pp. 2951-2960. ISSN 0126-6039 http://www.ukm.my/jsm/malay_journals/jilid47bil12_2018/KandunganJilid47Bil12_2018.html
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Kebangasaan Malaysia
building	UKM Institutional Repository
collection	Online Access
language	English
description	Metagenomic DNA library from palm oil mill effluent (POME) was constructed and subjected to high-throughput screening to find genes encoding cellulose- and xylan-degrading enzymes. DNA of 30 positive fosmid clones were sequenced with next generation sequencing technology and the raw data (short insert-paired) was analyzed with bioinformatic tools. First, the quality of 64,821,599 reverse and forward sequences of 101 bp length raw data was tested using Fastqc and SOLEXA. Then, raw data filtering was carried out by trimming low quality values and short reads and the vector sequences were removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained. The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de Bruijn graph algorithm. Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE, where 2139 scaffolds have been reconstructed. 16,386 genes have been identified after gene prediction using Prodigal and putative ID assignment with Blastp vs NR protein. The acceptable strategy to handle metagenomic NGS-data in order to detect known and potentially unknown genes is presented and we showed the computational efficiency of de Bruijn graph algorithm of de novo assembly to 21 bioprospect genes encoding cellulose-degrading enzymes and 6 genes encoding xylan-degrading enzymes of 30.3% to 100% identity percentage.
format	Article
author	Benbelgacem, Farah Fadwa Mohd Noor Mat Isa, Abdelrahim, Muhammad Alfatih Muddathir Afidalina Tumian, Bellag, Oualid Abdelkader Adibah Parman, Ibrahim Ali Noorbatcha, Hamzah Mohd Salleh,
spellingShingle	Benbelgacem, Farah Fadwa Mohd Noor Mat Isa, Abdelrahim, Muhammad Alfatih Muddathir Afidalina Tumian, Bellag, Oualid Abdelkader Adibah Parman, Ibrahim Ali Noorbatcha, Hamzah Mohd Salleh, Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome
author_facet	Benbelgacem, Farah Fadwa Mohd Noor Mat Isa, Abdelrahim, Muhammad Alfatih Muddathir Afidalina Tumian, Bellag, Oualid Abdelkader Adibah Parman, Ibrahim Ali Noorbatcha, Hamzah Mohd Salleh,
author_sort	Benbelgacem, Farah Fadwa
title	Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome
title_short	Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome
title_full	Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome
title_fullStr	Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome
title_full_unstemmed	Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome
title_sort	next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from pome metagenome
publisher	Penerbit Universiti Kebangsaan Malaysia
publishDate	2018
url	http://journalarticle.ukm.my/12915/ http://journalarticle.ukm.my/12915/ http://journalarticle.ukm.my/12915/1/03%20Farah%20Fadwa%20Benbelgacem.pdf
first_indexed	2023-09-18T20:03:40Z
last_indexed	2023-09-18T20:03:40Z
_version_	1777407015985872896

Next generation sequencing-data analysis for cellulose- and xylan-degrading enzymes from POME metagenome

Similar Items