Standards in Genomic Sciences (2011) 4:72-80 DOI:10.4056/sigs.1543845 The Genomic Standards Consortium Complete genome sequence of Cellulophaga algicola type strain (IC166T) Birte Abt1, Megan Lu2,3, Monica Misra2,3, Cliff Han2,3, Matt Nolan2, Susan Lucas2, Nancy Hammon2, Shweta Deshpande2, Jan-Fang Cheng2, Roxane Tapia2,3, Lynne Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Galina Ovchinikova2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, John C. Detter2,3, Evelyne Brambilla1, Manfred Rohde6, Brian J. Tindall1, Markus G��ker1, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Nikos C. Kyrpides2, Hans-Peter Klenk1, and Alla Lapidus2* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, 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 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences,The University of Queensland, Brisbane, Australia *Corresponding author: Alla Lapidus Keywords: aerobic, motile by gliding, Gram-negative, agarolytic, chemoorganotrophic, cold adapted enzymes, Flavobacteriaceae, GEBA Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within the phy- lum 'Bacteroidetes' and was isolated from Melosira collected from the Eastern Antarctic coastal zone. The species is of interest because its members produce a wide range of extra- cellular enzymes capable of degrading proteins and polysaccharides with temperature optima of 20-30��C. This is the first completed genome sequence of a member of the genus Cellulo- phaga. The 4,888,353 bp long genome with its 4,285 protein-coding and 62 RNA genes con- sists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain IC166T (= DSM 14237 = CIP 107446 = LMG 21425) is the type strain of Cellulophaga algicola, which belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes'. The strain was isolated from the surface of the chain-forming sea- ice diatom Melosira collected from the Eastern An- tarctic coastal zone, and was described by Bow- man in 2000 [1]. Currently, there are six species placed in the genus Cellulophaga, namely C. algico- la [1], C. baltica, C. fucicola, C. lytica [2], C. pacifica [3] and C. tyrosinoxydans [4]. C. lytica is the type species of the genus Cellulophaga [2]. The generic name of the genus derives from the Neo-Latin word 'cellulosum' meaning 'cellulose' and the Greek word 'phagein' meaning 'to eat', referring to an eater of cellulose. Here we present a summary classification and a set of features for C. algicola IC166T, together with the description of the com- plete genomic sequencing and annotation. Classification and features A representative genomic 16S rRNA sequence of C. algicola was compared using NCBI BLAST under default settings (e.g., considering only the high- scoring segment pairs (HSPs) from the best 250

Abt et al. http://standardsingenomics.org 73 hits) with the most recent release of the Green- genes database [5] and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem [6]) were determined. The five most frequent genera were Cellulophaga (39.5%), Maribacter (7.8%), Flavobacterium (5.6%), Cytophaga (5.4%) and Formosa (4.7%) (135 hits in total). Regarding the 21 hits to se- quences from members of the species, the average identity within HSPs was 95.8%, whereas the av- erage coverage by HSPs was 94.9%. Regarding the 16 hits to sequences from other members of the genus, the average identity within HSPs was 94.7%, whereas the average coverage by HSPs was 94.7%. Among all other species, the one yield- ing the highest score was C. baltica, which corres- ponded to an identity of 98.1% and a HSP cover- age of 97.8%. The highest-scoring environmental sequence was GU452686 ('sediments coast oil pol- luted Black Sea coastal sediment clone 70SZ2'), which showed an identity of 96.5% and a HSP coverage of 98.1%. The five most frequent key- words within the labels of environmental samples which yielded hits were 'marin' (4.7%), 'water' (4.3%), 'sediment' (4.3%), 'sea' (3.5%) and 'coastal' (2.6%) (115 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found. The environmental samples database (env_nt) contains the marine metagenome clone ctg_1101667042524 (AACY022635173) isolated from Sargasso Sea near Bermuda, sharing 92% identity with IC166T [7] (as of January 2011). Figure 1 shows the phylogenetic neighborhood of C. algicola IC166T in a 16S rRNA based tree. The sequences of the five 16S rRNA gene copies in the genome differ from each other by up to two nuc- leotides, and differ by up to 14 nucleotides from the previously published 16S rRNA sequence (AF001366), which contains nine ambiguous base calls. Figure 1. Phylogenetic tree highlighting the position of C. algicola IC166T relative to the other type strains within the family Flavobacteriaceae. The tree was inferred from 1,458 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] 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 support values from 350 bootstrap replicates [11] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [12] are shown in blue, published genomes in bold. The cells of C. algicola are generally rod-shaped with rounded or tapered ends with cell lengths and widths ranging from 1.5 to 4 and 0.4 to 0.5 ��m, respectively (Figure 2 and Table 1). C. algicola is motile by gliding [1]. Colonies on marine 2216 agar have yellow-orange pigmentation and a com- pact center, with a spreading edge possessing ligh- ter pigmentation. Their consistency is slimy and they are slightly sunken into the agar [1]. Flexiru- bin pigments are not formed. C. algicola grows be- tween 0.5 and 10% NaCl, with the best growth in the presence of about 2% NaCl. The temperature range for growth is between -2��C and 28��C, with an optimum between 15-20��C on solid media and at about 20-25��C in liquid media [1]. The optimal pH for growth is about 7.5 [1]. The organism is strictly aerobic and chemoorga- notrophic [1]. C. algicola can hydrolyze agar, starch, gelatine, carboxymethylcellulose (CMC), casein, Tween 80, tributyrin and L-tyrosine, but not urate, xanthine or dextran, when grown in presence of 1% L-tyrosine a reddish-brown diffus- ible pigment is formed [1]. Nitrate reduction is positive, whereas denitrification, H2S production and indole production are negative [1,18]. Acid is formed oxidatively from D-galactose, D-glucose, D- fructose, sucrose, cellobiose, lactose and mannitol. Strain IC166T is sensitive to ampicillin, streptomy- cin and carbenicillin and shows resistance to te- tracycline [3].