Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584

Abstract

Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario agricultural soil (Canada) with promising deoxynivalenol biotransformation capabilities. In addition, we report the draft genome of Devosia riboflavina strain IFO13584, used as a control strain in our studies aimed at highlighting unique gene clusters involved in deoxynivalenol epimerization.

GENOME ANNOUNCEMENT

Devosia as a genus has recently gained attention for the ability of many reported species to survive harsh environmental conditions, including hexachlorocyclohexane dump sites, diesel-contaminated soils, beach and deep-sea surface sediments, and alpine glacier cryoconite (1–12). Furthermore, a number of Devosia isolates have shown promising biodetoxification abilities that could lead to their utilization in agricultural and industrial applications as detoxifying agents (4, 13–16). Our laboratory recently reported the isolation of a new Devosia species, Devosia sp. strain 17-2-E-8 (IDAC 040408-1=ATCC PTA-121309) with a proposed designation of Devosia epimeris, which is capable of aerobically biotransforming deoxynivalenol (DON), a mycotoxin produced by various Fusarium species (15, 16). In our efforts to decipher the metabolic pathways responsible for this transformation, we report the de novo genome assemblies of two Devosia isolates: Devosia sp. strain 17-2-E-8 and D. riboflavina strain IFO13584 (ATCC 9526). D. riboflavina IFO13584 served as a control strain in these studies to highlight unique gene clusters in Devosia sp. 17-2-E-8 possibly involved in DON epimerization.

Genomic DNA from both isolates was purified using the Puregene Yeast/Bact. kit (Qiagen, Toronto, Canada) after 7 days of growth in LB broth and subjected to whole-genome sequencing using the MiSeq sequencer (Illumina, San Diego). Following fragmentation, end-repair, and sample indexing, a total of 17,343,120 and 15,745,680 of 300-bp paired-end reads were produced, resulting in 1,100× and 882× coverage for the Devosia sp. 17-2-E-8 and D. riboflavina IFO13584 genomes, respectively.

The FASTQC algorithm (17) was used to check the initial quality of our sequence reads. After removal of overrepresented sequences and quality trimming of the reads, de novo genome assemblies were generated using the CLC Genomics Workbench version 6.0.1 package. This resulted in a 4.7-Mb genome consisting of 125 contigs for Devosia sp. 17-2-E-8 and a 5.3-Mb genome consisting of 113 contigs for D. riboflavina IFO13584. Automated genome annotation was performed using both the RAST server (18) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP), which predicted 3,943 and 4,273 coding DNA sequences for Devosia sp. 17-2-E-8 and D. riboflavina IFO13584, respectively. An in-depth comparative genomic analysis of our data will be included in a future publication.

Nucleotide sequence accession numbers.

Both whole-genome shotgun assemblies of Devosia sp. 17-2-E-8 and D. riboflavina IFO13584 were deposited at DDBJ/EMBL/GenBank under the accession numbers JQGB00000000 and JQGC00000000, respectively.