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.
Highlights
Cyanobacteria are capable of converting carbon dioxide into oxygen via photosynthesis and have been proposed as significant players in the evolution of current atmospheric oxygen levels during the Precambrian era (Meeks et al 2001; Schirrmeister et al 2013) and as origin of chloroplasts via endosymbiosis with eukaryotic cells (Agapakis et al 2011; Chu et al 2004)
Nostoc punctiforme is a filamentous cyanobacterium found in the majority of illuminated environments and it plays a key role in the global nitrogen cycle through its facultative diazotrophic traits
Sequencing of bacterial genomes using Pacific Biosciences’s (PacBio’s) single molecule sequencing approach that simultaneously allows the detection of deoxyribonucleic acid (DNA) methylation patterns in bacterial genomes is routinely performed in many laboratories (Flusberg et al 2010; GomezEscribano et al 2016; Koren et al 2013)
Summary
Cyanobacteria are capable of converting carbon dioxide into oxygen via photosynthesis and have been proposed as significant players in the evolution of current atmospheric oxygen levels during the Precambrian era (Meeks et al 2001; Schirrmeister et al 2013) and as origin of chloroplasts via endosymbiosis with eukaryotic cells (Agapakis et al 2011; Chu et al 2004). The ample development of bioinformatics tools with various strategies for genome assembly and annotation has dramatically increased our ability to understand the biology of prokaryotes and eukaryotes at the genomic level and to mine their genomes for natural products (Weber et al 2015; Medema et al 2015; Yandell and Ence 2012). In this context, the objective of this study is to provide an update of the N. punctiforme genome through resequencing and reannotating of its genome with state-of-the-art technologies. The data presented here were generated and analyzed as part of Community Science Program
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