Genome of Lactobacillus plantarum strain DmelCS_001

Draft Genome Sequence of Lactobacillus plantarum DmelCS_001, isolated from the Gut of Drosophila melanogaster  Canton S

Jeanne Kagle1, John M. Chaston2, Peter D. Newell2, Chun-nin (Adam) Wong2, and Angela E. Douglas2

1Department of Biology, Mansfield University, Mansfield, PA, 2Department of Entomology, Cornell University, Ithaca, NY

 

Lactobacillus plantarum is frequently identified as a member of the gut microbiota of animals. Here we report the genome sequence of L. plantarum DmelCS001, isolated from the gut of Drosophila melanogaster. We assembled the genome with Velvet and annotated the genome using the RAST server, attaining a genome sequence of 88 contigs with 3,066 annotated features and a total of 3,195,557 bp.

Lactobacillus plantarum has been isolated most frequently from fermented foods, but has also been identified as a member of the gut microbiota of animals, including humans (Hammes and Vogel, 1995), mice (Marco et al., 2009),and drosophilid flies (Chandler et al., 2011; Cox and Gilmore, 2007; Sharon et al., 2010; Shin et al., 2011; Wong et al., 2011).  In humans, several studies have demonstrated beneficial probiotic effects of L. plantarum against irritable bowel syndrome (Niedzielin et al., 2001) and Clostridium difficile infection (Wullt et al., 2003).  The preservative and probiotic characteristics of Lactobacillus plantarum may be due in part to their production of bacteriocins called plantaricins (Diep et al., 2009; Lavermicocca et al., 2000).  In Drosophila melanogaster, L. plantarum promote the growth of larvae under low-nutrient conditions (Storelli et al., 2011) and influence mating preference (Sharon et al., 2010). 

Lactobacillus plantarum DmelCS_001 was isolated from aseptically dissected guts of Drosophila melanogaster (Canton-S) reared at 25°C on yeast-glucose diet (Wong et al., 2011), and maintained at 30° C on M.R.S. medium (de Man et al., 1960). Cultures were grown statically to late-log phase and genomic DNA prepared with the Qiagen DNeasy Blood and Tissue Kit as per the manufacturer’s recommendations and sequenced with Illumina HiSeq 2000 at The Cornell Life Sciences Core Facility.

We used a random subset of 25,000,000 quality filtered read-pairs providing x1565 genome coverage, for the assembly.  The genome was assembled using Velvet 1.2.03 (Zerbino and Birney, 2008) by randomly allocating each sequence to one of 10 subset files, each containing 2,500,000 read pairs (142X coverage per subset file).  Sequences from each subset file were assembled into contigs using kmer lengths of 83-85, aided by predictions of the Velvet Advisor tool (Seeman) and tests with multiple kmer lengths. The output contig file from each subset was used as input in a second velvet run with a kmer length of 83 to create a final assembly that was 3,188,535 bp long and represented by 98 contigs, with a maximum contig size of 282,956-bp and N50 of 124,826-bp. Annotation and subsequent analyses were performed using the Rapid Annotation using Subsystem Technology (RAST) server (Aziz et al., 2008) to create an annotated genome sequence with 3,195,557bp, 88 contigs, 3131 features, and an estimated 27 missing genes.

The genome of L. plantarum DmelCS_001 contains 3,195,557 bases with a G+C content of 44.5%. This is comparable to the three other available full genomes of L. plantarum (WCFSi, ST-III, and JDM1) with genome sizes 3.2-3.39 Mb and G+C content of 44.4–44.7%.  There is one predicted copy of each of the 16S and 23S rRNA genes, three predicted copies of the 5S rRNA gene and 60 predicted tRNAs.  Analysis with the RAST server revealed 3,066 predicted coding sequences in 494 subsystems.  As expected, genes coding all the fermentation pathways found in L. planatarumWCFS1 are also present in L. plantarum DmelCS_001.  L. plantarum DmelCS_001 also has the genetic capacity for anaerobic respiration, as for other members of this species.  The potential to use nitrate as a final electron acceptor for anaerobic respiration varies among the strains of L. plantarum for which complete genomes are available: unlike strains WCFS1 and JDM1 with the genetic potential to reduce nitrate, DmelCS_001and ST-III lack this capability.   A BLAST search of six plantaricin and bacteriocin precursor peptides from L. plantarum NC8 (Maldonado et al., 2004) revealed that five were represented in the L. plantarum DmelCS_001 genome with 100% amino acid identity.  The availability of this genome sequence will facilitate a more targeted approach to the investigation of the metabolic and ecological roles of L. plantarum in the gut microbiota of D. melanogaster.

The sequence file is available as Download (see sidebar on left).  If you need the data in a different format, please contact us.

Acknowledgements

This work was supported by sabbatical leave from Mansfield University to JK, a Ruth L. Kirschstein NRSA postdoctoral fellowship to PDN (1F32GM099374-01), NIH grant 1R01GM095372 to AED, and. We thank Peter Schweitzer for assistance with filtering reads and Madeline Galac for assistance installing Velvet.

 

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