Draft Whole-Genome Sequence and Annotation of Xenorhabdus griffiniae Strain BMMCB Associated with the South African Entomopathogenic Nematode Steinernema khoisanae Strain BMMCB.

Xenorhabdus griffiniae strain BMMCB (LDNM00000000) belongs to the family Enterobacteriaceae and was isolated from the South African entomopathogenic nematode Steinernema khoisanae strain BMMCB (GenBank accession no. KT027382). Here, we report the draft whole-genome sequence of X. griffinae strain BMMCB with a genome size of 4,183,779 bp and 44.7% G+C content. The NCBI Prokaryotic Automatic Annotation Pipeline (PGAAP) revealed 3,970 genes.

GENOME ANNOUNCEMENT

Xenorhabdus species are symbiotic Gram-negative bacteria which belong to the Enterobacteriaceae family and have a specific obligatory association with Steinernematid entomopathogenic nematodes (EPNs) (1). The EPN-bacteria complex holds great potential as biocontrol agents of insect pests (2). The Steinernematid EPN infective juvenile (IJ) gains entry through the natural openings of insect host larvae and regurgitate the Xenorhabdus bacterial endosymbiont into the hemolymph (1). Following infection, Xenorhabdus spp. depress the insect host’s immune system and release insecticidal metabolites, which are lethal to the insect (3). Bactericidal, fungicidal, and nematicidal compounds released by the bacteria facilitate the maintenance of a monoxenic environment within the infected host’s hemocoel (4–6). Several compounds with antibiotic activity secreted by Xenorhabdus spp. include benzylineacetone (7), xenorhabdins and xenocoumacin (8), phenethylamides (9), and cyclolipopeptide (10). In this study, we present the description of the X. griffiniae BMMCB draft whole-genome sequence and annotation.

X. griffiniae BMMCB was isolated from the hemolymph of Galleria mellonella larvae infected with the South African entomopathogenic nematode Steinernema khoisanae BMMCB (isolation methods are described in reference 11). Genomic DNA was extracted from colony bacterial cultures using the ZR Fungal/Bacteria DNA kit (catalogue D6005) and was purified with the DNA clean and concentrator −5 kit (catalogue D4013). The strain was identified through the amplification and sequencing of the 16S rDNA. On NCBI BLAST, the results showed a 98% similarity percentage to Xenorhabdus griffiniae and was named Xenorhabdus griffiniae strain BMMCB.

Illumina libraries were generated using the Illumina Nextera DNA sample preparation kit (FC-121-1031) and sequenced using an Illumina MiSeq instrument (version 3, chemistry 300 × 300 bp). CLC Genomic Workbench v7 (CLC bio) was used for quality trimming of adapter sequences and merging of overlapping paired reads. The X. griffiniae BMMCB genome was subsequently assembled de novo and 231 contigs (≥400 bp) were generated with an average coverage of 232×. The whole-genome sequence comprises 4,183,779 bp, with an N50 of 57,901 bp and G+C content of 44.7%, similar to those of other Xenorhabdus spp. (10). The assembly was submitted for annotation to the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) server (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). Annotation revealed a total of 3,970 genes (3,614 protein coding [CDs] and 271 pseudogenes). The genome has 12 rRNAs (5S, 16S, and 23S), 70 tRNAs, and 3 noncoding RNAs. The polyketide synthase genes involved in biosynthetic pathway of antibiotic compounds have been identified.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LDNM00000000. The version described in this paper is LDNM01000000.