Draft Genome Sequences of Two Bacteria from the Roseobacter Group

ABSTRACT

Here, we report the draft genome sequences of strains HS012 and HS039, which were isolated from cnidarian polyps that had recently undergone metamorphosis. Genomic analyses place these strains within the Phaeobacter and Leisingera genera, members of the Roseobacter group.

ANNOUNCEMENT

Strains HS012 and HS039 were isolated from artificial seawater containing Hydractinia symbiolongicarpus larvae that had spontaneously undergone metamorphosis to polyps. H. symbiolongicarpus colonies were generously provided by the Nicotra laboratory at the University of Pittsburgh. Strains were isolated from single colonies cultured on artificial seawater-tryptone (ASWT) agar medium (1) at 28°C for 48 h and subsequently were cultured in SWT liquid medium at 28°C for 24 h. Species identity was confirmed by 16S rRNA gene sequencing. Strains were grown in the same manner as for the isolation for DNA extraction.

Genomic DNA was extracted with a Zymo fungal/bacterial DNA miniprep kit and submitted to the Microbial Genome Sequencing Center (MiGS) (Pittsburgh, PA) for Illumina sequencing. The DNA libraries were prepared utilizing a single library preparation method based on the Illumina Nextera kit and were sequenced on the NextSeq 550 platform (2). We obtained paired-end reads (2 × 150 bp) totaling 1,312,670 reads covering a total of 355 Mb for HS012 and 1,817,862 reads covering a total of 473 Mb for HS039. The reads were submitted to the assembly and annotation service at PATRIC v3.6.9 (3) using Trim Galore v0.6.1 (4), Unicycler v0.4.8 (5), and the RAST tool kit (6) for trimming and assembly, with annotation performed via the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (7). Utilizing the EvalG tool as part of the PATRIC-based assembly (8), the genomes had completeness of 100% and 99.6% for HS012 and HS039, respectively. Phaeobacter sp. strain HS012 has a 4.2-Mb genome with a total GC content of 60%, with 26 contigs and an N₅₀ value of 461,505 bp. Leisingera sp. strain HS039 has a 5.0-Mb genome with a total GC content of 62%, with 196 contigs and an N₅₀ value of 60,120 bp. PATRIC predicted 4,108 and 5,137 coding sequences for HS012 and HS039, respectively. For the software utilized, default parameters were used except where otherwise noted.

Based on genomic analysis, strain HS012 is closely related to Phaeobacter inhibens strain P80 (9), with an average nucleotide identity (ANI) of 98% (10) (Fig. 1). Strain HS039 is closely related to Leisingera sp. strain ANG59, a strain isolated from the accessory nidamental gland of the Hawaiian bobtail squid (Euprymna scolopes) (11), with an ANI of 84% (Fig. 1). These species belong to the Roseobacter lineage (Rhodobacteraceae), a widespread Alphaproteobacteria group (12–16). Because the strains were initially isolated from H. symbiolongicarpus larvae that had spontaneously undergone metamorphosis, we searched the genomes for bacterial genes that had been previously implicated in the stimulation of metamorphosis. Both genomes lack homologs of genes known to induce metamorphosis of tubeworms via metamorphosis-associated contractile structures (17, 18) or corals via tetrabromopyrrole (19). Whether strain HS012 or strain HS039 stimulates H. symbiolongicarpus metamorphosis and produces other yet uncharacterized stimulatory bacterial products will be an interesting direction of future research.

FIG 1.

ANI genome-based distance matrix between isolates HS012 and HS039 and members of the Roseobacter clade. The ANI genome comparisons were performed using EzBioCloud (10). Numerical values in the matrix indicate percent similarity of nucleotides between the corresponding bacterial strains.

Data availability.

The genome sequencing and assembly projects for strains HS012 and HS039 in this work have been deposited in GenBank under SRA accession numbers SRR13962962 and SRR13962961, whole-genome sequencing genome accession numbers JAGEUG000000000 and JAGEUH000000000, and raw sequencing SRA accession numbers SAMN18268725 and SAMN18268726, respectively.