ABSTRACT
Here, we report the draft genome sequence of Aquicella lusitana DSM 16500T isolated from water in a spa at São Gemil, Portugal. Its genome of 2,529,370 bp encodes 2,437 predicted genes, of which 2,375 are protein-coding genes. It has at least one mobilizable plasmid.
KEYWORDS: waterborne pathogens, host-cell interactions
ANNOUNCEMENT
Members of the gammaproteobacterial genus, Aquicella, are commonly found in aquatic environments, require minimal oxygen, and are mesophilic chemoorganotrophs that grow in protozoan hosts. Aquicella lusitana DSM16500T, the type strain of the species, is a gram-negative, filamentous rod isolated from a spa in São Gemil, Portugal, sampled during a routine follow-up quality control enumeration of Legionella (1).
A. lusitana was sequenced as part of the DOE Joint Genome Institute One Thousand Microbial Genomes (Phase IV) project (2). DNA was ordered from the DSMZ DNA bank, Leibniz Institute. DNA was sheared to ~300 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburn, MA, USA). The DNA fragments were size-selected by double-solid phase reverse immobilization (SPRI), and selected fragments were end-repaired, A-tailed, and ligated with Illumina-compatible sequencing adapters from Integrated DNA Technologies (IDT, Coralville, IA, USA) containing unique molecular index barcodes for each sample library. The library was prepared on the Illumina HiSeq 2500 platform using a TruSeq paired-end cluster kit, v4, following a 2 × 150-bp indexed run recipe and Illumina’s cBot instrument to generate clustered flow cells for sequencing. A total of 7,097,274 reads were generated, producing 1,071,688,374 bp of sequence data. Raw reads were filtered for quality, adapters, and contaminants using BBTools v37.53 (3). The filtered and normalized reads were assembled using SPAdes (v3.10.1) (4), 200 bp was trimmed from all contig ends, and contigs with length < 1 kbp or read coverage < 2 were discarded using BBTools. The final draft assembly contained 68 contigs in 66 scaffolds, totaling 2,529,370 bp in size (Table 1). The organism’s closest sequenced relative is Aquicella siphonis (94.65% ribosomal RNA (rRNA) identity) and is distantly related to members of the Order Legionellales within the gammaproteobacteria (5). The final assembly was based on 1,051,272,564 bp of Illumina data with a genome coverage of 416× and was annotated using the IMG annotation pipeline (v. 4.15.2) (6), which predicted 2,375 protein-coding genes and 62 RNAs using tRNAScan-SE v.1.3.1, and the GeNomad v1.1.0 (7, 8) was employed to detect three fragmented plasmid contigs. AR.AGORN (v. 1.2.41), web version, was used for the confirmation of transfer RNAs (tRNAs) (9). Default parameters were used for all software.
TABLE 1.
De novo assembly and genome features of Aquicella lusitana
| Total scaffold sequence length (bp) | 2,529,370 |
|---|---|
| Number of contigs | 66 |
| Contig N50 (kb) | 94.8 |
| Average fold coverage (×) | 416 |
| GC content (%) | 44.19 |
| Total predicted genes | 2,437 |
| Predicted protein-coding genes | 2,375 |
| RNA genes | 62 |
| rRNA genes | 3 |
| 5S rRNA | 1 |
| 16S rRNA | 1 |
| 23S rRNA | 1 |
| tRNA genes | 46 (ARAGORN, 47) |
| Transfer-messenger RNA genes | 1 |
| Other RNA genes | 13 |
| CRISPR arrays | 0 |
| Provirus | 0 |
| Plasmid contigs | 3 (2756170232_000001, 2756170232_000002, 2756170232_000003) |
The first MOBF plasmid contig, 2756170232_000001, has mating pair formation components, the mob genes, and other conjugation genes. The second contig, 2756170232_000002, bears a T4SS protein and Ti-type conjugative transfer relaxase traA, with the genome possessing type IV assembly proteins. The third contig, 2756170232_000003, bears a Group II catalytic intron. The presence of a type II pilus assembly protein, type III pantothenate kinase, and type IV (Dot/Icm secretion systems, as in Legionella pneumophila and Coxiella burnetii) and type VI secretion systems confirms its adaptation to an intracellular, possibly pathogenic lifestyle. Genes involved in xenobiotic degradation are also detected.
ACKNOWLEDGMENTS
The work (proposal DOI: https://doi.org/10.46936/10.25585/60001087) was conducted by the U.S. Department of Energy Joint Genome Institute (JGI) (https://ror.org/04xm1d337), a Department of Energy Office of Science User Facility that is supported by the Office of Science of the U.S. Department of Energy, operated under contract number DE-AC02-05CH11231. This announcement was largely prepared by undergraduate students, and we gratefully acknowledge JGI for initiating and supporting it as an educational project (the “Adopt-a-genome” project).
Contributor Information
Imade Y. Nsa, Email: insa@unilag.edu.ng.
Rekha Seshadri, Email: rseshadri@IbI.gov.
David Rasko, University of Maryland Baltimore, Baltimore, Maryland, USA.
DATA AVAILABILITY
The high-quality draft genome annotation of Aquicella lusitana is available from the Joint Genome Institute IMG/M Taxon ID 2756170232. This Whole Genome Shotgun project has been deposited in GenBank under the accession number QQAX00000000; project data are available under BioProject accession number PRJNA442658, with BioSample accession number SAMN08776294, and Sequence Read Archive SRX4011438.
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Associated Data
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Data Availability Statement
The high-quality draft genome annotation of Aquicella lusitana is available from the Joint Genome Institute IMG/M Taxon ID 2756170232. This Whole Genome Shotgun project has been deposited in GenBank under the accession number QQAX00000000; project data are available under BioProject accession number PRJNA442658, with BioSample accession number SAMN08776294, and Sequence Read Archive SRX4011438.