Genome Sequences of Type Strains of Seven Species of the Marine Bacterium Pseudoalteromonas

Abstract

There are over 30 species in the marine bacterial genus Pseudoalteromonas. However, our knowledge about this genus is still limited. We sequenced the genomes of type strains of seven species in the genus, facilitating the study of the physiology, adaptation, and evolution of this genus.

GENOME ANNOUNCEMENT

The genus Pseudoalteromonas (Gammaproteobacteria, Alteromonadales, Alteromonadaceae) was proposed by Gauthier et al. (5) and is attracting much attention, because a number of Pseudoalteromonas species can produce a variety of compounds with antimicrobial, antifouling, algicidal, and various pharmaceutically relevant activities (3). There are over 30 species in the genus, all of which are found in the oceans. One interesting feature of the genus is that it can be divided into two clades: pigmented and nonpigmented species (3). The pigmented species tend to produce bioactive compounds, while the nonpigmented species generally have broader environmental tolerance than the pigmented ones (3). Currently, the genome sequences of over 10 strains are available in public databases (2, 7, 9–11). However, among the sequenced strains, only two (P. tunicata D2^T [10] and P. rubra ATCC 29570^T [11], both belonging to the pigmented clade) are type strains of Pseudoalteromonas species. Here, we present the genome sequences of seven type strains, including three from the pigmented clade (P. citrea NCIMB 1889^T, P. piscicida JCM 20779^T, and P. spongiae UST010723-006^T) and four from the nonpigmented clade (P. arctica A 37-1-2^T, P. haloplanktis ATCC 14393^T, P. marina mano4^T, and P. undina NCIMB 2128^T).

Genomes were sequenced using Illumina Solexa technology (1). A 500-bp Illumina paired-end library was prepared for each strain. The sequencing generated 520 Mb to 540 Mb of clean data for each strain. The average sequencing coverage ranged from 100-fold to 130-fold. Reads (read length, 90 bp) of each strain were assembled using SOAPdenovo, version 1.05 (6). Numbers of large contigs (>500 bp) were 114 for NCIMB 1889^T, 73 for JCM 20779^T, 14 for UST010723-006^T, 68 for A 37-1-2^T, 56 for ATCC 14393^T, 31 for mano4^T, and 20 for NCIMB 2128^T. The protein-coding open reading frames (ORFs) were predicted using Glimmer, version 3.02 (4) and were annotated using the Swiss-Prot, NCBI nr, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (8).

The genome sizes are 5.34 Mb for P. citrea NCIMB 1889^T (4,677 ORFs), 5.28 Mb for P. piscicida JCM 20779^T (4,782 ORFs), 4.72 Mb for P. spongiae UST010723-006^T (4,331 ORFs), 4.63 Mb for P. arctica A 37-1-2^T (4,242 ORFs), 5.02 Mb for P. haloplanktis ATCC 14393^T (4,441 ORFs), 4.18 Mb for P. marina mano4^T (3,863 ORFs), and 4.00 Mb for P. undina NCIMB 2128^T (3,689 ORFs). The G+C content ranges from 39.04% (P. arctica A 37-1-2^T) to 43.24% (P. piscicida JCM 20779^T). Comparisons of all sequenced Pseudoalteromonas genomes showed that, on average, the genomes of the pigmented strains (5.53 ± 0.57 Mb for 7 strains) were larger than those of the nonpigmented ones (4.39 ± 0.45 Mb for 15 strains).

The sequenced genomes of the type strains not only facilitate the study of the physiology, adaptation, and evolution of this genus but also provide a good resource for the study of the synthesis of the bioactive compounds by this genus.

Nucleotide sequence accession numbers.

The genome sequences of the seven strains were deposited in GenBank under accession numbers AHBY00000000, AHBZ00000000, AHCA00000000, AHCB00000000, AHCC00000000, AHCE00000000, and AHCF00000000.