Metagenomic Fosmid Library Sequencing

A total of 3,300 randomly selected fosmid clones were sequenced on one full lane of the 454 GS-FLX Genome Sequencer System using the Titanium platform (Roche, Brandford, CT, USA) following the manufacturer’s protocol. Repeats in raw sequenced reads obtained were removed using RepeatMasker (http://www.repeatmasker.org). The vector and host sequences were filtered by BLASTN, with an E-value cutoff of 1e-3. The filtered reads were assembled using the Newbler assembly software, developed by 454 Life Sciences (version 2.6, Roche). Non-overlapping fragment singletons were clustered using the CD-HIT software [58 (link)] to minimize redundant sequences. The overall process of metagenomic data preparation and analysis is summarized in Additional file 1: Figure S1. The entire sequences of the bagasse fosmid library have been deposited to the NCBI Sequence Read Archive (SRA), which can be accessed using the accession number: SRX493840.

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Mhuantong W., Charoensawan V., Kanokratana P., Tangphatsornruang S, & Champreda V. (2015). Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnology for Biofuels, 8, 16.

Publication 2015

Titanium platform Newbler assembly software

A 300 Bagasse Clones Genome Library Metagenomic Titanium Vector

Corresponding Organization : Mahidol University

Other organizations : National Center for Genetic Engineering and Biotechnology

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Variable analysis

independent variables

A total of 3,300 randomly selected fosmid clones

dependent variables

Sequenced on one full lane of the 454 GS-FLX Genome Sequencer System using the Titanium platform
Repeats in raw sequenced reads removed using RepeatMasker
Vector and host sequences filtered by BLASTN, with an E-value cutoff of 1e-3
Filtered reads assembled using the Newbler assembly software, developed by 454 Life Sciences (version 2.6, Roche)
Non-overlapping fragment singletons clustered using the CD-HIT software

control variables

Manufacturer's protocol for the 454 GS-FLX Genome Sequencer System using the Titanium platform
E-value cutoff of 1e-3 for BLASTN filtering
Newbler assembly software version 2.6 developed by 454 Life Sciences
CD-HIT software for clustering non-overlapping fragment singletons

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