Whole-genome sequence of Clostridium lituseburense L74, isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus.

Clostridium lituseburense L74 was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus collected in Yeong-dong, Chuncheongbuk-do, South Korea and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession NZ_LITJ00000000.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/assembly/GCF_001276215.1/

Experimental design, materials and methods

Insects are the most numerous species on the earth and inhabit various niches such as soil and water. Insect guts present distinctive environments for microbial colonization, and bacteria in the gut potentially provide many beneficial services to their hosts [1], [2]. Clostridium lituseburense L74 is already revealed from gut of hore fly, Haematobia irritans [3]. A Gram-positive staining, rod-shaped, non-motile, spore-forming anaerobic bacterium, was isolated from the larval gut of a rhinoceros beetle, Trypoxylus dichotomus and characterized. Genomic DNA was purified from 2-L cultures of C. lituseburens L74 [4]. The extracted DNA sample was extracted using bead-beating technique [5] and sequenced on HiSeq 2000 (Illumina). De novo genome assembly was performed using CLCbio CLC Genomics Workbench v7.5 and annotation was conducted on RAST [6]. SEED viewer was used for subsystem functional categorization of the predicted open reading frames (ORFs) and for visualization [7].

Data description

Whole genome sequences were generated through the HiSeq technique and were assembled into total 81 contigs. The genome consisted of 3,687,211 base pairs of double-stranded DNA with a GC content of 27.2%. The N50 of the genome was 123,171 bps. The genome was predicted to have 3328 coding sequence, 55 tRNAs and 2 rRNAs. These genes were annotated and classified into 364 subsystems (Fig. 1). Most of the annotated genes were involved in amino acids and derivatives (261), cofactors, vitamins, prosthetic groups and pigments formations (234), protein metabolism (225), RNA metabolism (167), and carbohydrate metabolism (165), respectively. Especially, the RAST results show that this bacteria genome carries 11 toxins and superantigens related with Streptolysin S Biosynthesis and transport genes. Considering that Streptolysin S is closely associated with bacterial diseases in human, further study is needed to clarify its pathogenesis.

Fig 1

Subsystems of Clostridium lituseburense L74 based on SEED database.

Nucleotide accession number

This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. NZ_LITJ00000000.

Conflict of interest

The authors clarified that this work and writing has no conflict of interest.

Specifications
Organism/cell line/tissue	Clostridium lituseburense
Strain	L74
Sequencer or array type	HiSeq (Illumina)
Data format	Analyzed
Experimental factors	Microbial strain
Experimental features	Whole genome analysis and gene annotation of L74
Consent	N/A
Sample source location	Larval gut of a rhinoceros beetle