Draft Genome of Phaeobacter gallaeciensis ANG1, a Dominant Member of the Accessory Nidamental Gland of Euprymna scolopes

Abstract

Phaeobacter gallaeciensis strain ANG1 represents the dominant member of the bacterial consortium within the reproductive accessory nidamental gland (ANG) of the squid Euprymna scolopes. We present a 4.59-Mb assembly of its genome, which may provide clues as to how it benefits its host.

GENOME ANNOUNCEMENT

The accessory nidamental glands (ANGs) of female cephalopods are reproductive organs containing dense consortia of bacteria dominated by Alphaproteobacteria from the Roseobacter clade (5, 11, 13). Although the function of this organ has not been demonstrated, the production of antimicrobial and/or antifouling compounds from ANG bacterial isolates has been proposed (4, 5). Here, we describe the draft genome of Phaeobacter gallaeciensis ANG1, a member of the Rhodobacteraceae, isolated from the ANG of a sexually mature Hawaiian bobtail squid, Euprymna scolopes.

The Roseobacter clade is a ubiquitous, diverse group that can comprise up to 20% of bacterial populations in marine environments (7). Besides being implicated in a number of large-scale ecological roles, i.e., carbon cycling (12) and sulfur metabolism (10), roseobacters are also found as members of many eukaryotic-bacterial symbioses. For example, they form obligate associations with marine algae (1), are major colonizers of corals (2), and are commonly found as dominant members in the ANGs of several cephalopods—including loliginid squid (5), cuttlefish (11), and the Hawaiian bobtail squid Euprymna scolopes (unpublished data).

We cultured three isolates from the ANG of E. scolopes and identified them by sequencing the full-length 16S rRNA gene. The isolate that was sequenced was Gram negative and positive for oxidase and catalase. The 16S rRNA gene was 99.7% identical to 16S gene sequences found in three separate E. scolopes ANG clone libraries and 99.2% identical to a coastal isolate, Phaeobacter gallaeciensis SCH0407, in GenBank (accession no. AY881240). The genome of this isolate, P. gallaeciensis ANG1, was sequenced using Illumina mated paired-end technology. A total of 1.73 × 10⁸ 36-bp reads were assembled using the CLC Genomic Workbench assembler (CLC Bio, Denmark), resulting in 1,370-fold coverage of a 4.59-Mb genome contained in 135 contigs. Glimmer (8), GeneMark (6), and the RAST server (3) were used to predict open reading frames (ORFs). A total of 4,389 protein-coding genes, 35 tRNAs, and one ribosomal operon were identified.

Phaeobacter gallaeciensis ANG1 has complete Embden-Myerhoff-Parnas, Entner-Doudoroff, and pentose phosphate pathways and a complete tricarboxylic acid (TCA) cycle. The genome contains an abundance of predicted ABC transporters, particularly for peptides, amino acids, and polyamines (i.e., putrescine, spermidine). Other transport systems include a twin-arginine transport system, the Sec pathway, and a type IV and a type VI secretion system. In addition, all cobalamin synthesis genes are present, suggesting that P. gallaeciensis ANG1 may provide this nutrient for its host. While there is high similarity to two other Phaeobacter gallaeciensis genomes available (strains BS107 and 2.10), strain ANG1 lacks the genes needed to synthesize the antibiotic tropodithietic acid (TDA) (9), and classical pathways for antibiotic production were not found.

This genome shows the metabolic and transport potential of a major bacterial constituent of the accessory nidamental gland of E. scolopes. Further analyses of this genome may provide significant clues to understanding the role of P. gallaeciensis in this symbiotic organ.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under accession no. AFCF00000000. The version described in this paper is the first version, AFCF01000000.