Standards in Genomic Sciences (2011) 4:173-182 DOI:10.4056/sigs.1644004 The Genomic Standards Consortium Complete genome sequence of Desulfurococcus mucosus type strain (O7/1T) Reinhard Wirth1, Olga Chertkov2,3, Brittany Held,2,3, Alla Lapidus2, Matt Nolan2, Susan Lucas2, Nancy Hammon2, Shweta Deshpande2, Jan-Fang Cheng2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Pagani Ioanna2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Yvonne Bilek1, Thomas Hader1, Manfred Rohde6, Stefan Spring7, Johannes Sikorski7, Markus G��ker7, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,8, Victor Markowitz4, Philip Hugenholtz2,9, Nikos C. Kyrpides2, and Hans-Peter Klenk7* 1 University of Regensburg, Archaeenzentrum, Regensburg, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI ��� Helmholtz Centre for Infection Research, Braunschweig, Germany 7 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA 9 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk Keywords: hyperthermophile, anaerobic, organotroph, sulfur respiration, spheroid-shaped, non-motile, extracellular enzymes, Desulfurococcaceae, GEBA Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus Desulfuro- coccus, which belongs to the crenarchaeal family Desulfurococcaceae. The species is of in- terest because of its position in the tree of life, its ability for sulfur respiration, and several bio- technologically relevant thermostable and thermoactive extracellular enzymes. This is the first completed genome sequence of a member of the genus Desulfurococcus but already the 8th sequence from a member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain O7/1T (= DSM 2162 = ATCC 35584 = JCM 9187) is the type strain of the species Desulfuro- coccus mucosus [1], which is the type species of its genus Desulfurococcus. The genus currently con- sists of five validly named species [2]. For the ge- nus name the Neo-Latin 'desulfo-' meaning 'desulfuricating, is used to characterize the dissi- milatory sulfate-reducing feature of this spheroid- shaped 'coccus' [2]. The species epithet is derived from the Latin word 'mucosus' (slimy) [2]. Strain O7/1T was isolated from an acidic hot spring in Askja, Iceland and the name of the species was effectively published by Zillig et al. in 1982 [2] valid publication of the name followed in 1983 [3]. The strain was an early target for phylogenetic studies of the domain Archaea (at that time termed ���Archaebacteria���) via DNA-rRNA cross- hybridizations [4,5], as well as studies on the arc- haeal DNA-dependent RNA polymerase structure [6] and Archaea-specific quinones [7]. Subse- quently, strain O7/1T was used for studies on thermostable extracellular enzymes such as pro-

Desulfurococcus mucosus type strain (O7/1T) 174 Standards in Genomic Sciences teinase [8] and pullulanase [9]. Here we present a summary classification and a set of features for D. mucosus strain O7/1T, together with a description of the complete genome sequencing and annota- tion. Classification and features The single genomic 16S rRNA sequence of strain O7/1T was compared using NCBI BLAST under de- fault settings (e.g., considering only the high- scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Green- genes database [10] and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem [11]) were determined. The five most frequent genera were Sulfolobus (27.8%), Aeropyrum (11.3%), Desulfurococcus (11.3%), Igni- coccus (6.5%) and Vulcanisaeta (6.2%) (100 hits in total). Regarding the five hits to sequences from other members of the genus, the average identity within HSPs was 96.7%, whereas the average cov- erage by HSPs was 97.4%. Among all other species, the one yielding the highest score was Desulfuro- coccus mobilis, which corresponded to an identity of 100.0% and an HSP coverage of 100.0%. The highest-scoring environmental sequence was AB462558 ('Microbial production and energy source hyperthermophilic prokaryotes geothermal hot spring pool clone DDP-A01'), which showed an identity of 95.8% and a HSP coverage of 98.2%. The five most frequent keywords within the labels of environmental samples which yielded hits were 'spring' (9.2%), 'microbi' (6.8%), 'hot' (6.2%), 'nation/park/yellowston' (5.4%) and 'popul' (4.8%) (150 hits in total), indicating a good fit to the original habitat of D. mucosus. Environmental samples which yielded hits of a higher score than the highest scoring species were not found. Figure 1 shows the phylogenetic neighborhood of D. mucosus in a 16S rRNA based tree. A 16S rRNA reference sequence for D. mucosus has not been previously published. Figure 1. Phylogenetic tree highlighting the position of D. mucosus relative to the other type strains within the fam- ily Desulfurococcaceae. The tree was inferred from 1,334 aligned characters [12,13] of the 16S rRNA gene se- quence under the maximum likelihood criterion [14] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are sup- port values from 1,000 bootstrap replicates [15] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [16] are shown in blue, Staphylothermus hellenicus CP002051 and published ge- nomes in bold [17-22].