Abstract
The draft genomes of Thermus tengchongensis YIM 77401 and T. caliditerrae YIM 77777 are 2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes, respectively. Gene content and growth experiments demonstrate broad metabolic capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation, incomplete denitrification, and polysulfide reduction.
GENOME ANNOUNCEMENT
Bacterial strains YIM 77401 and YIM 77777, members of the order Thermales, class Deinococci, were isolated from Frog Mouth Spring (Hamazui), Rehai National Park, Tengchong County, Yunnan Province, China (1). The draft genomes of the two strains were generated at the DOE Joint Genome Institute (JGI), Walnut Creek, California, USA, using Pacific Biosciences (PacBio) technology. A PacBio SMRTbell library was created and sequenced using the PacBio RS platform, which generated 191,522 filtered subreads totaling 522 Mbp for strain YIM 77401, and 280,439 filtered subreads totaling 626 Mbp for strain YIM 77777. HGAP version: 2.0.0 (2) was used to assemble raw reads. Genome annotation was performed using the JGI Prokaryotic Automatic Annotation Pipeline (3) with manual curation using GenePRIMP (4) and additional manual review using the Integrated Microbial Genomes–Expert Review (IMG-ER) platform (5). JGI’s library construction and sequencing protocols can be found at http://www.jgi.doe.gov.
The strain YIM 77401 genome encoded 2,726 predicted genes in 5 contigs, including 47 tRNA-encoding genes and 3 rRNA operons, and the strain YIM 77777 genome encoded 2,305 predicted genes in 4 contigs, including 50 tRNA-encoding genes and 3 rRNA operons. Both genomes included at least one megaplasmid (>100 kb), based on the presence of plasmid replicon domains (6). Analysis of carbohydrate-active enzymes (CAZymes) found in the strain YIM 77401 and YIM 77777 genomes revealed 39 and 32 CAZymes, respectively. Among these were 11 and 9 glycoside hydrolases (GHs) in strains YIM 77401 and YIM 77777, respectively, including GHs predicted for starch hydrolysis (GH13 and GH57) in both strains. This is consistent with amylase activity observed in both isolates. The genome of YIM 77401 featured genes involved in arsenite oxidation (aioAB), consistent with arsenite oxidation activity observed in this isolate. Both genomes contained a sox gene cluster composed of 10 genes (soxABCDFVWXYZ), predicted for thiosulfate oxidation (7), similar to other Thermus spp. (8–10); however, thiosulfate oxidation activity was only detected in YIM 77777.
Strain YIM 77401 contained a chromosomally encoded nitrate reductase gene cluster (narGHJIK) and two nitrate-nitrite transporters (narK1 and narK2), similar to other Thermus spp. (9). Genes encoding the catalytic subunit of a cd-cytochrome nitrite reductase (nirS) and nitric oxide reductase (norBC) were also found in this genome. However, nitrous oxide reductase (nos) genes, which catalyze the reduction of nitrous oxide to dinitrogen, were absent, consistent with the incomplete denitrification phenotype found in several Thermus spp. (9, 11) and the production of N2O as the terminal denitrification product by YIM 77401. Additionally, YIM 77401 and YIM 77777 contained genes for polysulfide reduction (psrABC), which is similar to other Thermus genomes (9) and consistent with polysulfide reductase activity in both isolates.
Nucleotide sequence accession numbers.
These whole-genome shotgun projects have been deposited in GenBank under accession numbers JQNC01000001 to JQNC01000004 (YIM77777) and JQLK01000001 to JQLK01000005 (YIM77401). The genome sequence is available from GenBank (NZ_JQNC00000000; GI: 740207912) for Thermus caliditerrae YIM77777, and from GenBank (NZ_JQLK00000000; GI:740202250) for T. tengchongensis YIM77401. The data are also available at the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) system (12).
ACKNOWLEDGMENTS
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. Additional support was supported by NSF grant no. OISE-0968421 to Brian P. Hedlund, and by the Key Project of International Cooperation of Ministry of Science and Technology (MOST) (no. 2013DFA31980) and Natural Science Foundation of China (no. 31470139) to Wen-Jun Li.
Funding Statement
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. Additional support was provided by NSF grant no. OISE-0968421 to Brian P. Hedlund and grants from the Key Project of International Cooperation of Ministry of Science & Technology (MOST) (no. 2013DFA31980) and the Natural Science Foundation of China (no. 31470139) to Wen-Jun Li.
Footnotes
Citation Mefferd CC, Zhou E-M, Yu T-T, Ming H, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Woyke T, Li W-J, Hedlund BP. 2016. High-quality draft genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, isolates from Tengchong, China. Genome Announc 4(2):e00312-16. doi:10.1128/genomeA.00312-16.
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