Draft Genome Sequence of the Brazilian Cyanobium sp. Strain CACIAM 14.

Given the scarcity of data pertaining to whole-genome sequences of cyanobacterial strains isolated in Brazil, we hereby present the draft genome sequence of the Cyanobium sp. strain CACIAM 14, isolated in southeastern Amazonia.

GENOME ANNOUNCEMENT

Given their ability to synthesize a wide variety of biologically active products (1–3), the cyanobacteria have played a relevant role in modern biotechnology. Their full biotechnological potential (4, 5) might be more easily exploited with knowledge of genetic content. We have reconstructed the genome of a cyanobacterial species by means of a bioinformatics pipeline applied to reads obtained from a non-axenic culture of a Cyanobium sp. Data are scarce pertaining to genomes of cyanobacteria isolated in Brazil, with currently only a few strains sequenced (6, 7).

We have hereby applied a next-generation sequencing pipeline according to Albertsen et al. (8) in order to obtain the genomic data pertaining to the Cyanobium sp. strain CACIAM 14, a unicellular cyanobacterium which was isolated from a water sample collected in December 2010 in the Tucuruí Hydroelectric Dam (3°49′55″S, 49°38′50″W) in the State of Pará, Brazil.

Two genomic DNA samples cultured 6 months apart were obtained from a non-axenic cyanobacterial biomass. The two nonpaired libraries were sequenced using the GS FLX 454 platform (Roche Life Science), yielding 660,228 (~255 Gb) and 815,325 (~357 Gb) reads for the first and second runs, respectively.

The datasets were assembled separately with Newbler 2.6 (minimum read size, 45 bp; minimum overlap, 40 bp; minimum overlap identity, 90%). These assemblies generated 3,654 and 3,256 contigs larger than 1 kb in length, with N50 values of 2,149 bp and 37,998 bp.

The contigs were identified and separated using a metagenomic assembling pipeline (8) for each putative organism, i.e., the isolated cyanobacterium and its associated heterotrophic bacterium (9, 10). The assembled contigs from the second run were used to determine the genome coverage.

Our analyses permitted the recovery of a draft genome which contains 71 contigs (total of ~3.2 Mb), ranging from 5,275 to 403,256 bp. The average coverage was 25×, with an assembly N50 of 61,937 bp and GC content of 68.56%.

The pipeline (8) used applied 107 hidden Markov models for essential genes present in a single copy in 95% of all bacteria. The genome draft sequence we present contains 108 of these genes, including duplications of the TIGR00436 and TIGR02350 genes. There is usually duplication of TIGR00436 only.

Structural annotation was carried out with the Prokaryotic Genome Annotation Pipeline (PGAP) tool, available on the NCBI website (11), resulting in 2,935 annotated coding sequences (CDSs) and 40 tRNA genes. The rRNA clusters were predicted by the RNAmmer tool (12). 16S rRNA was, however, found to be missing from this version of the draft sequence. Taxonomical identification was thus carried out based on the polymorphisms of the alpha and beta subunits of phycocyanin (according to Dall’Agnol et al. [13]), which presented 93% and 88% nucleotide identity, respectively, to those of Cyanobium gracile PCC 6307.

A preliminary analysis of the draft genome sequence using the antiSMASH tool (14) revealed the presence of 3 terpene clusters and 4 bacteriocin synthesis clusters.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JMRP00000000. The version described in this paper is version JMRP01000000.