Draft Genome Sequence of Stenotrophomonas bentonitica BII-R7T, a Selenite-Reducing Bacterium Isolated from Spanish Bentonites

ABSTRACT The Gram-negative bacterium Stenotrophomonas bentonitica BII-R7T was isolated from bentonite formations. Like other species within the genus Stenotrophomonas, strain BII-R7T possesses high tolerance to numerous heavy metals, suggesting potential for bioremediation purposes. The draft genome sequence reported here comprises 4.37 Mb with a G+C content of 66.5% and 3,796 predicted protein-coding sequences.

After cultivation on LB medium, genomic DNA of S. bentonitica BII-R7 T was extracted as described by Martín-Platero et al. (23). A genomic library with an insert size of 350 bp was sequenced using the Illumina HiSeq 2000 platform at Macrogen, Inc. (Seoul, Republic of Korea).
A total of 53,608,108 paired-end 101-bp reads were obtained (Ͼ1,000 ϫ coverage). The quality of the reads was assessed using FastQC (24), and the Q20 and Q30 indices were 95.34% and 87.69%, respectively. Multiple de novo genome assemblies were performed using ABySS version 1.5.1 (25) with k-mer sizes between 19 and 95. The assemblies were merged, filtered, and further assembled into scaffolds using TransABySS (26) and GS de novo assembler software (Roche). We obtained 191 scaffolds with an N 50 of 35,432 and an L 50 of 38. The mean size of these scaffolds was 22,890 bp with the largest comprising 187,875 bp and the smallest comprising 2,262 bp. The size of the entire sequence was 4,371,992 bp with a 66.5% GϩC content, which are values in accordance with described Stenotrophomonas spp.
Gene prediction and annotation were performed using the Rapid Annotations using Subsystems Technology server (27) and the Prokaryotic Genome Annotation Pipeline (28). The genomic features of S. bentonitica BII-R7 T included a total of 3,786 coding sequences (CDSs), 1 complete rRNA cluster, 44 tRNAs, 4 ncRNAs, and 158 pseudogenes. The coding sequences were classified into 431 subsystems, the most abundant of which were for the metabolism of amino acid derivatives (n ϭ 352 CDSs); carbohydrates (n ϭ 214); protein metabolism (n ϭ 205); metabolism of cofactors, vitamins, prosthetic groups, and pigments (n ϭ 204); membrane transport (n ϭ 160); and RNA metabolism (n ϭ 147). Additionally, 115 of these coding sequences were related to stress responses, such as osmotic and oxidative stress, cold and heat shock stress, or uptake of selenate and selenite. Genes related to degradation or resistance to a variety of toxic compounds (e.g., ethidium bromide) and heavy metals (e.g., cobalt, zinc, cadmium, tellurium, copper, arsenic, or mercury) were also identified in the present draft genome. Moreover, the draft genome contains specific enzymes, such as alkaline and acid phosphatases or glutathione reductases, which could, respectively, be involved in the high levels of tolerance that S. bentonitica BII-R7 T (1,17) has to uranium and selenium.
Accession number(s). This whole-genome shotgun project has been deposited at GenBank/ENA/DDBJ under the accession number MKCZ00000000. The version described in this paper is the first version, MKCZ01000000.

ACKNOWLEDGMENTS
This study was supported by the ERDF-cofinanced grants CGL2012-36505 and CGL2014-59616-R (Ministerio de Ciencia e Innovación, Spain; 80% funded by FEDER). We also acknowledge funding received from the Euratom research and training program 2014 -2018 under grant agreement no. 661880.