ABSTRACT
Serratia marcescens is a Gram-negative bacterium causally linked to acroporid serratiosis, a form of white pox disease implicated in the decline of elkhorn corals. We report draft genomes of 38 S. marcescens isolates collected from host and nonhost sources. The availability of these genomes will aid future analyses of acroporid serratiosis.
ANNOUNCEMENT
Serratia marcescens is a widely distributed Gram-negative bacillus within the Enterobacteriaceae family (1). The species has long been recognized as an important pathogen of humans (1, 2), insects (3–5), and plants (6). Two ecotypes (pulsed-field gel electrophoresis [PFGE] types PDL100 and PDR60) were identified as causative agents of acroporid serratiosis (a form of white pox disease) in reef-building Acropora palmata corals (7, 8). Given the ecological importance of A. palmata, it is imperative to gain a better understanding of the genetic mechanisms underlying acroporid serratiosis and what sets the PDL100 and PDR60 ecotypes apart from other pathogenic strains.
Thirty-five S. marcescens PDR60 isolates were collected from a range of host (A. palmata) and nonhost (Siderastrea siderea and Solenastrea bournoni corals, corallivorous snail Coralliophila abbreviata, and wastewater) sources throughout the Florida Keys National Marine Sanctuary (Table 1) (8–10). The WWI31 isolate (obtained from wastewater influent) was virulent against A. palmata but had a novel PFGE pattern (8). The PDL100 isolate was obtained previously from diseased A. palmata in 1999 (7), and the ATCC 13880 isolate was obtained by others from pond water in the Czech Republic and deposited to ATCC in 1961. Starting with glycerol stocks, each isolate was streaked onto Trypticase soy agar plates (37°C overnight), and isolated colonies were grown in lysogeny broth (37°C overnight with shaking). Total DNA for Illumina sequencing was isolated using a Qiagen DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA) per the manufacturer’s instructions. Genomic DNA for PacBio sequencing was isolated using a cetyltrimethylammonium bromide protocol (11). Illumina sequencing libraries were prepared using a PCR-free TrueSeq DNA kit (Illumina, San Diego, CA, USA) and sequenced at Hudson Alpha Institute for Biotechnology (Huntsville, AL, USA) using paired-end chemistry with 250-bp (EL1 and EL119), 150-bp (EL1, EL119, and KS10), or 100-bp (remaining 35 isolates) read lengths. Additionally, six isolates (EL1, EL116, EL119, EL41, EL60, and KS10) were also sequenced on three PacBio single-molecule real-time (SMRT) cells at the Interdisciplinary Center for Biotechnology Research (University of Florida, Gainesville, FL, USA). Adapter sequences and low-quality bases were removed from Illumina reads with TrimGalore! version 0.4.0 (options, -paired and -retain_unpaired) (12). The processed reads were assembled de novo with Velvet version 1.2.10 (options -scaffolding, no; -exp_cov, 80; -cov_cutoff, 10; -min_contig_lgth, 500) (13) using the k-mer sizes listed in Table 1. Hybrid assemblies were constructed with MaSuRCA version 3.2.1 (options, default) (14) using the mean insert sizes and insert size standard deviations calculated with BWA (15). Assembly metrics were determined using QUAST version 5.0.2 (options, default) (16). All genomes were annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) (17).
Accession numbers, genome assembly metrics, and sources for the 38 S. marcescens isolatesa
Table 1 shows summaries of the 38 draft genome assemblies. The availability of these genomes will aid in more comprehensive analyses of S. marcescens and acroporid serratiosis.
Data availability.This whole-genome shotgun project has been deposited in GenBank under the accession numbers listed in Table 1. The raw sequence reads were deposited in the Sequence Read Archive under the BioProject accession numbers PRJNA494152 (nonhybrid assemblies) and PRJNA438529 (hybrid assemblies).
ACKNOWLEDGMENT
This project was funded by NSF-NIH Ecology of Infectious Disease program grants EF1015342 (awarded to Erin K. Lipp and John P. Wares) and EF1015032 (awarded to Kathryn P. Sutherland).
FOOTNOTES
- Received 19 February 2019.
- Accepted 4 March 2019.
- Published 4 April 2019.
- Copyright © 2019 Elledge et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
