Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones, Isolated from Malaysian Tropical Soil

Abstract

Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.

GENOME ANNOUNCEMENT

Dyella japonica is a Gram-negative, rod-shaped bacterium of the family Xanthomonadaceae that was first isolated by Xie and Yokota (11) and designated as a new genus and new species. In 2007, a patient who received long-term hemodialysis was infected by this environmental soil bacterium (7). In this study, Dyella japonica strain A8 was isolated using a published method (3). Quorum quenching represents a novel anti-infective therapy measure (5), but such activity has not been reported in any member of the Dyella genus. Here we present the whole-genome shotgun sequence of Dyella japonica strain A8.

Genomic DNA of Dyella japonica strain A8 was isolated using the QIAamp DNA minikit (Qiagen, Germany) according to the manufacturer's protocol. The quality of DNA was examined using the NanoDrop spectrophotometer (Thermo Scientific) and Qubit 2.0 fluorometer (Life Technologies). The whole-genome sequencing of Dyella japonica strain A8 was performed using the Illumina HiSeq 2000 next-generation DNA platform (Illumina, Inc., CA) after the construction of a sequencing library derived from a 150-bp paired-end library.

Sequences were trimmed and de novo assembled using Genomics Workbench version 5.1 (CLC bio, Aarhus, Denmark), which yielded 5,355,354 reads from 206 contigs with approximately 88-fold coverage. The N₅₀ quality measurement of the contigs was 52 kb, with an average contig size of 23 kb, and the largest contig assembled was approximately 224 kb. The genome contains 437,387,597 bp, with a G+C content of 64.7%. Prodigal version 2.60 (6) was performed to predict open reading frames (ORFs), resulting in 4,365 ORFs, and these ORFs were further annotated by comparison with NCBI-NR and Blast2GO (4). A total of 49 tRNAs were predicted using tRNAscan-SE (v.1.21) (9). One complete rRNA operon, one copy each of a 5S rRNA gene, a 23S rRNA gene, and a 16S rRNA gene, was identified using RNAmmer (8).

BLASTX against a quorum-quenching lactonase database acquired from the UniProtKB protein knowledgebase (1) was performed to search for possible N-acylhomoserine lactone (AHL)-degrading genes. One predicted protein-coding sequence (CDS) which encodes 264 amino acids shows 81% similarity to the reported attM gene, an AHL-degrading gene (2, 10). The genome sequence of Dyella japonica strain A8 may provide insights into the quorum-quenching activity of this soil bacterium.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ALOY00000000. The version described in this paper is the first version, ALOY01000000.