Journal of Biotechnology 219 (2016) 22–23 Contents lists available at ScienceDirect Journal of Biotechnology j ournal homepage: www.elsevier.com/locate/jbiotec Genome announcement T Complete genome sequence of Agarivorans gilvus WH0801 , an agarase-producing bacterium isolated from seaweed a,1 b,1 c a b Pujuan Zhang , Junpeng Rui , Zongjun Du , Changhu Xue , Xiangzhen Li , a,∗ Xiangzhao Mao a College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China b Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China c College of Marine Science, Shandong University at Weihai, Weihai 264209, China a r t i c l e i n f o a b s t r a c t T Article history: Agarivorans gilvus WH0801 , an agarase-producing bacterium, was isolated from the surface of sea- Received 1 December 2015 weed. Here, we present the complete genome sequence, which consists of one circular chromosome Accepted 10 December 2015 of 4,416,600 bp with a GC content of 45.9%. This genetic information will provide insight into biotechno- Available online 12 December 2015 logical applications of producing agar for food and industry. © 2015 Elsevier B.V. All rights reserved. Keywords: Agarivorans gilvus Agarase Complete genome sequence Seaweed SMRT sequencing Agar, which is a phycocolloid extracted from the cell wall of a Members of the aerobic genus Agarivorans, affiliated to - group of red algae (Rhodophyceae), is composed of agarose and Proteobacteria, have the ability to produce agarase and catalyze the T agaropectin (Fu and Kim, 2010). The structure of agarose is com- hydrolysis of agar. Recently, a novel strain WH0801 was isolated ␤ posed of repetitive units of 3-O-linked -D-galactopyranose and from the surface of seaweed in the shallow coastal region of Weihai, ␣ 4-O-linked 3, 6-anhydro- -l-galactose. Agaropectin has the same China, proposed to be a new species Agarivorans gilvus (Du et al., basic disaccharide-repeating units as agarose, except for its sul- 2011). Two novel ␤-agarase genes, AgWH50A and AgWH50C, and fate esters, pyruvate acetal and methyl ethers groups. As a type a novel ␣-neoagarobiose hydrolase gene, AgaWH117, were cloned of marine polysaccharide, agar could be hydrolyzed to prepare from this strain by our group (Liu et al., 2014a,b, 2015). oligosaccharides which will broaden its applications in the food, The whole genome sequence was conducted with a single- cosmetic, and pharmaceutical industries (Yang et al., 2014). Agar- molecule real-time (SMRT) sequencing platform PacBio RS II degrading organisms were first reported by Gran in 1902 (Swartz (Pacific Biosciences, USA). Totally 488,799,626 bp of quality- and Gordon, 1959). Since then, at least 30 bacteria with this capacity controlled reads were de novo assembled using the RS Hierarchical have been identified (Weiner et al., 2008). Agar-degrading organ- Genome Assembly Process (HGAP) protocol version 3.0 in SMRT isms have been isolated from many sources, such as seawater, Analysis version 2.3.0 (Pacific Biosciences, USA). Protein-coding marine sediments, marine algae, marine mollusks, fresh water, and sequences (CDS), tRNA, and rRNA genes were predicted with Glim- soils. Agarases activity have been examined in several bacteria, mer 3.0 (Delcher et al., 1999), tRNAscan-SE (Lowe and Eddy, 1997), including Alteromonas sp., Pseudomonas sp., Vibrio sp., Cytophaga and RNAmmer (Lagesen et al., 2007), respectively. The functional sp., Agarivorans sp., Thalassomonas sp., Pseudoalteromonas sp., Bacil- annotation and metabolic pathway analysis were achieved on the lus sp., and Acinetobacter sp., etc (Fu and Kim, 2010). Expert Review version of the Integrated Microbial Genomes system (IMG ER) (Markowitz et al., 2009). T The complete genome sequence of A. gilvus WH0801 consists of a single 4,416,600 bp chromosome with a GC content of 45.9%, including 4279CDSs, 22 rRNAs, 91 tRNAs and 9 miscellaneous RNAs ∗ Corresponding author. Fax: +86 532 82032272. (Table 1). The genome includes two ␤-agarase genes and three E-mail address: [email protected] (X. Mao). 1 glycosyl hydrolase genes. These authors contributed equally to this work. http://dx.doi.org/10.1016/j.jbiotec.2015.12.007 0168-1656/© 2015 Elsevier B.V. All rights reserved. P. Zhang et al. / Journal of Biotechnology 219 (2016) 22–23 23 Table 1 References T Genome features of Agarivorans gilvus WH0801 . Delcher, A.L., Harmon, D., Kasif, S., White, O., Salzberg, S.L., 1999. Improved Feature Value microbial gene identification with GLIMMER. Nucleic Acids. Res. 27, Genome size (bp) 4,416,600 4636–4641. G + C content (%) 45.9 Du, Z.J., Lv, G.Q., Rooney, A.P., Miao, T.T., Xu, Q.Q., Chen, G.J., 2011. Agarivorans Protein-coding genes (CDS) 427,9 gilvus sp. nov. isolated from seaweed. Int. J. Syst. Evol. Microbiol. 61, 493–496. Fu, X.T., Kim, S.M., 2010. Agarase: review of major sources, categories, purification rRNA (5S, 16S, 23S) 22 method, enzyme characteristics and applications. Mar. Drugs 8, 200–218. tRNA 91 Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. Miscellaneous RNA 9 RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Liu, N., Mao, X., Du, Z., Mu, B., Wei, D., 2014a. Cloning and characterisation of a This is the first report on complete genome sequence of A. novel neoagarotetraose-forming-beta-agarase, AgWH50A from Agarivorans gilvus. This genomic information will provide the second reference gilvus WH0801. Carbohydr. Res. 388, 147–151. Liu, N., Mao, X., Yang, M., Mu, B., Wei, D., 2014b. Gene cloning, expression and genome data set of genus Agarivorans, help better understanding characterisation of a new beta-agarase, AgWH50C, producing neoagarobiose the agar production pathway in the biofilm of the seaweed surface, from Agarivorans gilvus WH0801. World J. Microbiol. Biotechnol. 30, and provide insights into biotechnological applications of the strain 1691–1698. Liu, N., Yang, M., Mao, X., Mu, B., Wei, D., 2015. Molecular cloning and expression of producing agar for food and industry. a new alpha-neoagarobiose hydrolase from Agarivorans gilvus WH0801 and enzymatic production of 3,6-anhydro-l-galactose. Biotechnol. Appl. Biochem., Nucleotide sequence accession number http://dx.doi.org/10.1002/bab.1363. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of T transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. The complete genome sequence of A. gilvus WH0801 has been Markowitz, V.M., Mavromatis, K., Ivanova, N.N., Chen, I.M.A., Chu, K., Kyrpides, N.C., deposited in GenBank under the accession number CP013021. The 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25, 2271–2278. strain is available from the Agricultural Research Service Culture Swartz, M.N., Gordon, N., 1959. Agarase from an agar-digesting bacterium. J. Collection under the accession number of NRRL B-59247. Bacteriol. 77, 403–409. Weiner, R.M., Nd, T.L., Henrissat, B., Hauser, L., Land, M., Coutinho, P.M., Rancurel, Acknowledgements C., Saunders, E.H., Longmire, A.G., Zhang, H., 2008. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2–40. PLoS Genet. 4, 231–237. This work was supported by the National Natural Science Yang, M., Mao, X., Liu, N., Qiu, Y., Xue, C., 2014. Purification and characterization of two agarases from Agarivorans albus OAY02. Process Biochem. 49, 905–912. Foundation of China (31471607 and 31271923), the Fundamen- tal Research Funds for the Central Universities (201564018) and the International Postdoctoral Exchange Fellowship Program (20140075)..