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Genome Announc. 2017 September; 5(37): e00964-17.
Published online 2017 September 14. doi:  10.1128/genomeA.00964-17
PMCID: PMC5597761

Complete Genome Sequence of Spiroplasma corruscae EC-1T (DSM 19793), a Bacterium Isolated from a Lampyrid Beetle (Ellychnia corrusca)

ABSTRACT

Spiroplasma corruscae EC-1T (DSM 19793) was isolated from the gut of a lampryid beetle (Ellychnia corrusca) collected in Beltsville, MD, USA, in 1983. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma species.

GENOME ANNOUNCEMENT

Spiroplasma corruscae is known to be associated with firefly beetles (Coleoptera: Lampyridae) and tabanid flies (Diptera: Tabanidae) in North America (1). EC-1T was isolated from the gut of a lampryid beetle (Ellychnia corrusca) collected in Beltsville, MD, USA, in 1983 and was designated the representative of group XIV within the genus. To facilitate future investigation on the biology of this bacterium, as well as to improve the taxon sampling of available Spiroplasma sequences for comparative genomics and evolutionary studies (2), we determined the complete genome sequence of S. corruscae EC-1T.

The strain was acquired from the German Collection of Microorganisms and Cell Cultures (catalog number DSM 19793). The freeze-dried sample was processed according to the manufacturer’s instruction and cultured in the M1D medium (3) prior to DNA extraction using the Wizard Genomic DNA purification kit (Promega, USA). PCR and Sanger sequencing were performed to verify that the 16S rRNA gene sequence matched the reference record (GenBank accession number AY189128) (4).

The procedures for genome sequencing, assembly, and annotation were based on those described in our previous studies (5,14). Briefly, we utilized the Illumina MiSeq platform to obtain 301-bp sequencing reads from one paired-end library with approximately 550-fold coverage. The initial de novo assembly was performed using Velvet version 1.2.10 (15). Subsequently, PAGIT version 1 (16) was used to assist an iterative process for improving the assembly. For each iteration, the raw reads were mapped to the assembly using the Burrows-Wheeler Alignment (BWA) tool version 0.7.12 (17), programmatically checked using the mpileup program in SAMtools package version 1.2 (18), and visually inspected using Integrative Genomics Viewer (IGV) version 2.3.57 (19). Polymorphic sites and gaps were corrected based on the mapped reads. The process was repeated until the complete genome sequence was obtained. The programs RNAmmer (20), tRNAscan-SE (21), and Prodigal (22) were used for gene prediction. The gene names and product descriptions were first annotated based on the homologous genes in other Spiroplasma genomes (5,14) as identified by OrthoMCL (23). Subsequent manual curation was based on the information obtain from the BlastKOALA tool (24) and BLASTp (25) searches against the NCBI nonredundant database (26). Putative clustered regularly interspaced short palindromic repeats (CRISPRs) were identified using CRISPRFinder (27).

The complete genome sequence of Spiroplasma corruscae EC-1T consists of one circular chromosome (1,175,400 bp; 25.4% G+C) and one plasmid (29,239 bp; 23.9% G+C). The first version of annotation includes one set of 16S-23S-5S rRNA genes, 29 tRNA genes (covering all 20 amino acids), 1,039 protein-coding genes, and one pseudogene. No putative plectroviral sequence or CRISPR element was found.

Accession number(s).

The complete genome sequence of Spiroplasma corruscae EC-1T has been deposited at DDBJ/EMBL/GenBank under the accession numbers CP022535 (chromosome) and CP022536 (plasmid).

ACKNOWLEDGMENTS

The bacterial strain was imported under permit number 103-B-001 issued by the Council of Agriculture of Taiwan. The Sanger sequencing service and the Illumina sequencing library preparation service were provided by the Genomic Technology Core (Institute of Plant and Microbial Biology, Academia Sinica). The Illumina MiSeq sequencing service was provided by the DNA Sequencing Core (Institute of Molecular Biology, Academia Sinica).

The funding for this project was provided by the Institute of Plant and Microbial Biology at Academia Sinica and the Ministry of Science and Technology of Taiwan (NSC 101-2621-B-001-004-MY3 and MOST 104-2311-B-001-019) to C.-H.K. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Footnotes

Citation Tsai Y-M, Lo W-S, Kuo C-H. 2017. Complete genome sequence of Spiroplasma corruscae EC-1T (DSM 19793), a bacterium isolated from a lampyrid beetle (Ellychnia corrusca). Genome Announc 5:e00964-17. https://doi.org/10.1128/genomeA.00964-17.

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