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AMB Express. 2017 Dec;7(1):42. doi: 10.1186/s13568-017-0338-9. Epub 2017 Feb 16.

Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production.

Author information

1
Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA, 95616, USA.
2
Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
3
ZeaChem, Boardman, OR, 97818, USA.
4
Washington State University, Richland, WA, 99354, USA.
5
Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA, 95616, USA. mhess@ucdavis.edu.
6
Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA. mhess@ucdavis.edu.

Abstract

Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy's IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.

KEYWORDS:

Carbon cycle; Cyanobacteria; Natural product synthesis; Nitrogen cycle; Nostoc punctiforme; Single molecule real-time sequencing

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