Complete Genome Sequence of a Coastal Cyanobacterium, Synechococcus sp. Strain NIES-970.

Members of the cyanobacterial genus Synechococcus are abundant in marine environments. To better understand the genomic diversity of marine Synechococcus spp., we determined the complete genome sequence of a coastal cyanobacterium, Synechococcus sp. NIES-970. The genome had a size of 3.1 Mb, consisting of one chromosome and four plasmids.

GENOME ANNOUNCEMENT

Synechococcus is a morphologically defined genus composed of unicellular, spherical- to rod-shaped cyanobacteria (1) that have a polyphyletic origin (2). Marine Synechococcus spp. are distributed over a range of environments, from coastal to pelagic, and Synechococcus spp., which belong to the same clade as Prochlorococcus spp., are known to be the most common and dominant species in pelagic oceans (3). However, the genetic and biological diversities of coastal Synechococcus spp. consisting of polyphyletic groups are still not understood. Here, we present the genome sequence of Synechococcus sp. NIES-970, a coastal cyanobacterium strain isolated from a tidal mud flat at Rikuhama Beach, Tokunoshima Island, Kagoshima, Japan in 1998, and maintained in the Microbial Culture Collection at the National Institute for Environmental Studies (http://mcc.nies.go.jp).

A paired-end library and a mate-pair library of 8-kb inserts were prepared using a Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA) and a Nextera mate-pair sample preparation kit (Illumina), respectively. These libraries were sequenced on a MiSeq sequencer (Illumina) with the MiSeq Reagent kit version 3 (600 cycles; Illumina). The output reads were filtered based on a 17-mer frequency using ShortReadManager (4) and then de novo assembled using Newbler version 2.9 (Roche Applied Science, Penzberg, Germany), which yielded 16 large contigs (>500 bp) and seven scaffolds. The average depth of sequence coverage was calculated to be 185-fold. The gap sequences were determined in silico using GenoFinisher and AceFileViewer (4), and the genome was found to consist of five circular structures, probably one chromosome and four plasmids. The total genome size was 3,123,859 bp, and the G+C content was 49.4%. Prediction of protein-coding genes, rRNA genes, and tRNA genes using Prokka (5) estimated 2,943, six, and 44 genes, respectively. Annotations of the predicted protein-coding genes were then conducted using original computer scripts that refer to the manually curated annotations in CyanoBase (6).

Synechococcus sp. NIES-970 was closely related to Synechococcus sp. NKBG15041c (7), with a 16S rDNA sequence of NIES-970 that was completely identical to that of NKBG15041c. We conducted reciprocal protein BLASTs between deduced protein sequences of Synechococcus sp. NIES-970 and NKBG15041c using BLAST+ version 2.3.0 (8), and the bidirectional BLAST best-hit pairs with query coverage ≥90% and percentage of identical matches ≥50 were considered as orthologous. The number of orthologs was 2,628, accounting for 89.3% of deduced proteins in Synechococcus sp. NIES-970. Furthermore, the results of the reciprocal protein BLASTs revealed that Synechococcus sp. NIES-970 has a putative copper-resistance, gene-regulating, two-component sensor histidine kinase CopS (locus_tag; NIES-970_28860) and a response regulator CopR (locus_tag; NIES-970_28880), which were located on a plasmid; however, NKBG15041c does not have these orthologs. The BLAST identity scores of the putative CopS and CopR to those of Synechocystis sp. PCC 6803 (9) were only 47% and 63%, respectively; however, putative copper-resistance protein-coding genes (locus_tag; NIES-970_28920 and NIES-970_28930), which were also not found on the NKBG15041c genome, were located near the copS and copR genes. Based on the genetic differences, NIES-970 may have higher copper-resistance ability than NKBG15041c.

Accession number(s).

The genome sequence of Synechococcus sp. NIES-970 has been deposited in DDBJ/EMBL/GenBank under the accession numbers AP017959 to AP017963.