Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and "Thermoanaerobacter cellulolyticus".

The genus Caldicellulosiruptor contains extremely thermophilic, cellulolytic bacteria capable of lignocellulose deconstruction. Currently, complete genome sequences for eleven Caldicellulosiruptor species are available. Here, we report genome sequences for three additional Caldicellulosiruptor species: Rt8.B8 DSM 8990 (New Zealand), Wai35.B1 DSM 8977 (New Zealand), and "Thermoanaerobacter cellulolyticus" strain NA10 DSM 8991 (Japan).

GENOME ANNOUNCEMENT

Lignocellulose-degrading microorganisms are of considerable interest for their use in the production of fuels and chemicals from renewable feedstocks. The genus Caldicellulosiruptor contains the most thermophilic, plant biomass–degrading bacteria isolated thus far, with optimal growth temperatures between 70 and 78°C (1). To date, complete genome sequences are available for 11 Caldicellulosiruptor species (1–7). From this information, it was determined that the Caldicellulosiruptor pan genome is still open, indicating that there is additional diversity within the genus, potentially involving yet-to-be discovered biomass-degrading enzymes and pathways. In light of this, three Caldicellulosiruptor isolates previously isolated from terrestrial hot springs were genome sequenced. Two were isolated from sites in New Zealand: Caldicellulosiruptor sp. strain Rt8.B8 DSM 8990 and strain Wai35.B1 DSM 8977 from Rotorua and Waimangu, respectively (8). The third, from Nozawa Hot Spring, Nagano Prefecture, Japan, was originally classified as “Thermoanaerobacter cellulolyticus” strain NA10 DSM 8991 (9, 10), although its genome sequence indicates that it belongs to the genus Caldicellulosiruptor.

The draft genomes of T. cellulolyticus NA10, Caldicellulosiruptor sp. strain Rt8.B8, and Caldicellulosiruptor sp. strain Wai35.B1 were produced by constructing Pacific Biosciences (PacBio) SMRTbell libraries, sequencing on the PacBio RS platform (11), and correcting errors on the Illumina platform for each microorganism at the DOE Joint Genome Institute (JGI). This generated 81,181, 150,202, and 166,964 filtered subreads totaling 349.1, 591.3, and 670.4 Mbp for T. cellulolyticus NA10, Caldicellulosiruptor sp. strain Rt8.B8, and Caldicellulosiruptor sp. strain Wai35.B1, respectively. All raw reads were accumulated via HGAP (12) and classified into genes using Prodigal (13) along with GenePRIMP (14). The predicted coding regions were then checked against the National Center for Biotechnology Information (NCBI), UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases to annotate the genomes within the Integrated Microbial Genomes (IMG) platform (http://img.jgi.doe.gov). Specific genes, such as tRNAs, rRNAs, and other noncoding RNAs, were identified by searching the genome with the tRNAScanSE tool (15), SILVA rRNA gene models (16), and INFERNAL (http://infernal.janelia.org).

The final draft assembly of T. cellulolyticus NA10 DSM 8991 contained 12 contigs in 12 scaffolds, totaling 2,514,985 bp, with an input read coverage of 88.9×. The final draft assembly of Caldicellulosiruptor sp. strain Rt8.B8 contained 2 contigs in 2 scaffolds, totaling 2,488,483 bp in size, with an input read coverage of 165.6×. Lastly, the final draft assembly of Caldicellulosiruptor sp. strain Wai35.B1 contained 1 contig in 1 scaffold, totaling 2,834,482 bp in size, with an input read coverage of 175.6×. The G+C content was 35.39%, 36.49%, and 35.78% for T. cellulolyticus NA10, Caldicellulosiruptor sp. strain Rt8.B8, and Caldicellulosiruptor sp. strain Wai35.B1, respectively. We expect that the novel features we are identifying in these genomes will further contribute to our understanding of the metabolic diversity of lignocellulolytic capabilities within the Caldicellulosiruptor genus.

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers LACN00000000, LACO00000000, and LACM00000000 for T. cellulolyticus NA10 DSM 8991, Caldicellulosiruptor sp. strain Rt8.B8 DSM 8990, and Caldicellulosiruptor sp. strain Wai35.B1 DSM 8977, respectively. The versions described in this paper are versions LACN01000000, LACO01000000, and LACM01000000.