Complete Genome Sequence of a Copper-Resistant Bacterium from the Citrus Phyllosphere, Stenotrophomonas sp. Strain LM091, Obtained Using Long-Read Technology.

The Stenotrophomonas genus shows great adaptive potential including resistance to multiple antimicrobials, opportunistic pathogenicity, and production of numerous secondary metabolites. Using long-read technology, we report the sequence of a plant-associated Stenotrophomonas strain originating from the citrus phyllosphere that displays a copper resistance phenotype.

GENOME ANNOUNCEMENT

The genus Stenotrophomonas (Gammaproteobacteria) is composed of ubiquitous bacteria mostly found associated with plants and soil (1). Members of the genus Stenotrophomonas are known for their wide ecological niche range and their great phenotypic versatility including opportunistic pathogenicity to humans and resistance to many antimicrobials. For S. maltophilia, this high adaptability has been associated with a large number of genomic islands differing between strains and conferring them various adaptive traits (1).

Here, we sequenced the Stenotrophomonas sp. strain LM091 that was collected in Réunion (South West Indian Ocean) from the citrus phyllosphere. The strain possesses a copper-resistant phenotype genetically related to that reported for different plant pathogens in the Xanthomonas genus (2).

Sequencing was operated with PacBio RSII, using one single-molecule real-time (SMRT) cell. Resulting raw reads were assembled de novo using SMRT Analysis HGAP v2.3 protocol with default parameters followed by a circularization step based on a combination of the minimus assembler (3) and the SMRT Analysis resequencing v1 protocol. The assembly yielded a single circularized contig of 4,317,450 bp with a G+C content of 66.7%, a mean coverage of 229, and a predicted number of coding sequences (CDS) of 3,800.

The 16S rDNA sequence was 100% identical to that of S. rhizophila strain QL-P4 and 99.8% identical to that of S. rhizophila type strain DSM14405. As advised in Figueras et al. (4), we calculated the average nucleotide identity (ANI) (program available at https://github.com/DamienFr/) scores with all the chromosome sequences of type Stenotrophomonas strains available to date. As the ANI scores were always inferior to the 95% species ANI cutoff value (ranging from 80.2 to 87.6%), this strain could not be assigned to any of the valid Stenotrophomonas species nor to putative new species recently studied (5). The most closely related species were S. rhizophila type strain DSM14405 (87.6%) and S. maltophilia type strain MTCC434 (84.3%).

LM091 comprises a 43-kb long chromosome-borne Tn3-like transposon encoding for the copLAB gene system. This system, demonstrated to confer a copper-resistant phenotype, was previously identified on plasmids from several Xanthomonas (6). In Réunion, this adaptive transposon was also found in the same niche in the citrus pathogen Xanthomonas citri pv. citri, suggesting putative transfers of genetic elements between these two genera, as previously proposed (7). The nucleotide sequence of the copper-resistance transposon of LM091 is 97.7% identical to that of Xanthomonas citri pv. citri. The sequence presented here is part of the sequencing effort necessary to further understand the putative implication of strains of Stenotrophomonas in the transfer of genes conferring resistance to antimicrobials.

Accession number(s).

The genome sequence has been deposited at GenBank under the GenBank accession no. CP017483.