Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station

The draft genome sequences of six Bacillus strains, isolated from the International Space Station and belonging to the Bacillus anthracis-B. cereus-B. thuringiensis group, are presented here. These strains were isolated from the Japanese Experiment Module (one strain), U.S. Harmony Node 2 (three strains), and Russian Segment Zvezda Module (two strains). Among the six Bacillus cereus sensu lato strains reported here, three U.S. Harmony Node 2 isolates (ISSFR-3F, ISSFR-9F, and ISSFT-23F) and one Japanese Experiment Module isolate (JEM-2) were sequenced and assembled with both Illumina MiSeq and PacBio RSII sequence data. The remaining assemblies, including two Russian isolates, were sequenced and assembled with only MiSeq data. The MiSeq runs yielded on average 24 to 54 million 300-bp reads (from 1,402 to 3,093 average coverage), while PacBio yielded 4,000 to 116,000 reads (from 7 to 202 average coverage) (Table 1). Due to the extremely high coverage ( 1,000 ), Illumina MiSeq reads were randomly down-sampled to 100 using an estimated genome size of 5.3 Mb, resulting in an average of 1.2 to 1.5 million paired-end reads per isolate. Next, the down-sampled reads were assembled using iMetAMOS (1) with IDBA_UD and SPAdes (2). IDBA_UD was selected as the best assembly for all six isolates. Low confidence bases within the selected IDBA_UD (3) assemblies were masked out by mapping all reads to the assembled contigs and detecting conflicting variants with FreeBayes (4). The PacBio reads were assembled following the methods described by Berlin et al. (5) with Celera Assembler version 8.3rc1 and polished with Quiver (6). A second round of polishing was performed post-Quiver using the available MiSeq data as input to Pilon (7). The six International Space Station (ISS) isolates were aligned (NUCmer [8], Parsnp [9]) against members of the B. cereus sensu lato group genomes (10). The PacBio assemblies were used for all isolates with sufficient read coverage, and Illumina assemblies were used for the remaining isolates. Based on genome size estimates (5.2 to 5.3 Mb), NUCmer pairwise alignments ( 99.9% average pairwise nucleotide identity) and maximum-likelihood phylogenetic placement, all six isolates were found to exhibit a very high degree of similarity. Received 31 May 2017 Accepted 5 June 2017 Published 10 August 2017 Citation Venkateswaran K, Checinska Sielaff A, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy A, Klubnik J, Treangen TJ, Rosovitz MJ, Bergman NH. 2017. Draft genome sequences from a novel clade of Bacillus cereus sensu lato strains, isolated from the International Space Station. Genome Announc 5:e00680-17. https://doi . org/10.1128/genomeA.00680-17. Copyright © 2017 Venkateswaran et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Kasthuri Venkateswaran, kjvenkat@jpl.nasa. gov, or Nicholas H. Bergman, nicholas.bergman@nbacc.dhs. gov. * Present address: Sergey Koren and Adam Phillippy, Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA. T.J.T. , M.J.R. , and N.H. B. contributed equally to this article. PROKARYOTES