Complete Genome Sequence of Seawater Bacterium Glaciecola nitratireducens FR1064^T

Abstract

Glaciecola nitratireducens strain FR1064^T was isolated from seawater and described as a new species by Baik et al. in 2006. The genome size is about 1.01 to 1.26 Mb smaller than two reported Glaciecola genomes, indicating the gain or loss of large genome segments in the evolution of Glaciecola strains.

GENOME ANNOUNCEMENT

The genus Glaciecola (Gammaproteobacteria, Alteromonadales, Alteromonadaceae), whose name means habitant of ice, was originally proposed to accommodate two Gram-negative, aerobic, psychrophilic, and seawater-requiring species isolated from Antarctic sea ice (3). However, as new species from this genus were found in diverse habitats (1, 3–5, 8, 11, 13, 14, 16, 17, 19, 20), it appears that, like many other genera of Gammaproteobacteria (Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia), bacteria from this genus live widely in global oceans. Currently, there are 10 recognized species in the Glaciecola genus. Phylogenetic analysis showed that the 10 species appeared in two lineages, with lineage I including Glaciecola punicea (the type species), G. pallidula, and G. nitratireducens and lineage II including the seven other species (20). Recently, the complete genome sequences of two strains from lineage II, Glaciecola sp. strain 4H-3-7+YE-5 (closely related to G. agarilytica NO2^T, with almost identical 16S rRNA genes) and G. mesophila, were reported (8, 18). However, no genome sequences for lineage I were reported.

G. nitratireducens strain FR1064^T (= KCTC 12276^T = JCM 12485^T) is a strain from Glaciecola lineage I. It was isolated from seawater off Jeju Island, Republic of Korea, and described as a new species by Baik et al. in 2006 (1). Here, we report the complete genome sequence of strain FR1064^T.

The genome of strain FR1064^T was sequenced using a combination of Roche/454 shotgun (10) and Illumina Solexa (2) technologies. A 454 shotgun library generated 363,715 reads, totaling 41.1 Mb, which represents 30 times the average genome coverage, and a 500-bp Illumina paired-end library produced 3,333,334 reads (read length, 90 bp), totaling 300 Mb, which represents 73 times the average genome coverage. The 454 shotgun reads were first assembled into 16 contigs using Newbler, version 2.3. The 454 shotgun contigs and Solexa paired-end reads were then assembled together using SOAPdenovo, version 1.05 (9), resulting in 16 contigs in 10 scaffolds. A total of 27 PCRs were performed to close the gaps between the contigs. The protein-coding open reading frames (ORFs) were predicted using Glimmer, version 3.02 (6), and were annotated using the Swiss-Prot, NCBI nr, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (12). The tRNA genes were predicted using the tRNAScan-SE search server (15). A comprehensive annotation and comparative genome analysis are under way.

The G. nitratireducens FR1064^T genome is contained in one chromosome with a total size of 4,134,229 bp, which is smaller than those of the two sequenced lineage II strains, G. mesophila (5,144,318 bp) and Glaciecola sp. 4H-3-7+YE-5 (5,393,591 bp). The G+C content is 42.3%. The genome contains 3,654 protein-coding ORFs, four rRNA operons, and 54 tRNA genes.

The G. nitratireducens FR1064^T genome represents the first sequenced genome for Glaciecola lineage I. The large difference in size between the FR1064^T genome and the G. mesophila and Glaciecola sp. 4H-3-7+YE-5 genomes makes FR1064^T a good model not only for the study of evolution of genome structure but also for the study of the genus' adaptation to very diverse marine habitats.

Nucleotide sequence accession number.

The data for the genome sequence of FR1064^T were deposited in GenBank under the accession number CP003060.