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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)


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.


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).


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.


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.


1. Hackett KJ, Whitcomb RF, French FE, Tully JG, Gasparich GE, Rose DL, Carle P, Bové JM, Henegar RB, Clark TB, Konai M, Clark EA, Williamson DL 1996. Spiroplasma corruscae sp. nov., from a firefly beetle (Coleoptera: Lampyridae) and tabanid flies (Diptera: Tabanidae). Int J Syst Bacteriol 46:947–950. doi:.10.1099/00207713-46-4-947 [PubMed] [Cross Ref]
2. Lo W-S, Huang Y-Y, Kuo C-H 2016. Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiol Rev 40:855–874. doi:.10.1093/femsre/fuw028 [PMC free article] [PubMed] [Cross Ref]
3. Whitcomb RF, Tully JG, McCawley P, Rose DL 1982. Application of the growth inhibition test to Spiroplasma taxonomy. Int J Syst Bacteriol 32:387–394. doi:.10.1099/00207713-32-4-387 [Cross Ref]
4. Gasparich GE, Whitcomb RF, Dodge D, French FE, Glass J, Williamson DL 2004. The genus Spiroplasma and its non-helical descendants: phylogenetic classification, correlation with phenotype and roots of the Mycoplasma mycoides clade. Int J Syst Evol Microbiol 54:893–918. doi:.10.1099/ijs.0.02688-0 [PubMed] [Cross Ref]
5. Lo W-S, Chen L-L, Chung W-C, Gasparich GE, Kuo C-H 2013. Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics 14:22. doi:.10.1186/1471-2164-14-22 [PMC free article] [PubMed] [Cross Ref]
6. Ku C, Lo W-S, Chen L-L, Kuo C-H 2013. Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma. Genome Biol Evol 5:1151–1164. doi:.10.1093/gbe/evt084 [PMC free article] [PubMed] [Cross Ref]
7. Lo W-S, Ku C, Chen L-L, Chang T-H, Kuo C-H 2013. Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biol Evol 5:1512–1523. doi:.10.1093/gbe/evt108 [PMC free article] [PubMed] [Cross Ref]
8. Ku C, Lo W-S, Chen L-L, Kuo C-H 2014. Complete genome sequence of Spiroplasma apis B31T (ATCC 33834), a bacterium associated with May disease of honeybees (Apis mellifera). Genome Announc 2(1):e01151-13. doi:.10.1128/genomeA.01151-13 [PMC free article] [PubMed] [Cross Ref]
9. Chang T-H, Lo W-S, Ku C, Chen L-L, Kuo C-H 2014. Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biol Evol 6:500–509. doi:.10.1093/gbe/evu033 [PMC free article] [PubMed] [Cross Ref]
10. Paredes JC, Herren JK, Schüpfer F, Marin R, Claverol S, Kuo C-H, Lemaitre B, Béven L 2015. Genome sequence of the Drosophila melanogaster male-killing Spiroplasma strain MSRO endosymbiont. mBio 6:e02437-14. doi:.10.1128/mBio.02437-14 [PMC free article] [PubMed] [Cross Ref]
11. Lo W-S, Gasparich GE, Kuo C-H 2015. Found and lost: the fates of horizontally acquired genes in arthropod-symbiotic Spiroplasma. Genome Biol Evol 7:2458–2472. doi:.10.1093/gbe/evv160 [PMC free article] [PubMed] [Cross Ref]
12. Lo W-S, Lai Y-C, Lien Y-W, Wang T-H, Kuo C-H 2015. Complete genome sequence of Spiroplasma litorale TN-1T (DSM 21781), a bacterium isolated from a green-eyed horsefly (Tabanus nigrovittatus). Genome Announc 3(5):e01116-15. doi:.10.1128/genomeA.01116-15 [PMC free article] [PubMed] [Cross Ref]
13. Lo W-S, Liu P-Y, Kuo C-H 2015. Complete genome sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a bacterium isolated from soldier beetle (Cantharis carolinus). Genome Announc 3(5):e01253-15. doi:.10.1128/genomeA.01253-15 [PMC free article] [PubMed] [Cross Ref]
14. Lo W-S, Gasparich GE, Kuo C-H 2016. Complete genome sequence of Spiroplasma turonicum Tab4cT, a bacterium isolated from horse flies (Haematopota sp.). Genome Announc 4(5):e01010-16. doi:.10.1128/genomeA.01010-16 [PMC free article] [PubMed] [Cross Ref]
15. Zerbino DR, Birney E 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi:.10.1101/gr.074492.107 [PubMed] [Cross Ref]
16. Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD 2012. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 7:1260–1284. doi:.10.1038/nprot.2012.068 [PMC free article] [PubMed] [Cross Ref]
17. Li H, Durbin R 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. doi:.10.1093/bioinformatics/btp324 [PMC free article] [PubMed] [Cross Ref]
18. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing Subgroup 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. doi:.10.1093/bioinformatics/btp352 [PMC free article] [PubMed] [Cross Ref]
19. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP 2011. Integrative genomics viewer. Nat Biotechnol 29:24–26. doi:.10.1038/nbt.1754 [PMC free article] [PubMed] [Cross Ref]
20. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi:.10.1093/nar/gkm160 [PMC free article] [PubMed] [Cross Ref]
21. Lowe TM, Eddy SR 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. [PMC free article] [PubMed]
22. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi:.10.1186/1471-2105-11-119 [PMC free article] [PubMed] [Cross Ref]
23. Li L, Stoeckert CJ, Roos DS 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189. doi:.10.1101/gr.1224503 [PubMed] [Cross Ref]
24. Kanehisa M, Sato Y, Morishima K 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. doi:.10.1016/j.jmb.2015.11.006 [PubMed] [Cross Ref]
25. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL 2009. Blast+: architecture and applications. BMC Bioinformatics 10:421. doi:.10.1186/1471-2105-10-421 [PMC free article] [PubMed] [Cross Ref]
26. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW 2016. GenBank. Nucleic Acids Res 44:D67–D72. doi:.10.1093/nar/gkv1276 [PMC free article] [PubMed] [Cross Ref]
27. Grissa I, Vergnaud G, Pourcel C 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. doi:.10.1093/nar/gkm360 [PMC free article] [PubMed] [Cross Ref]

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