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Draft Genome Sequence of Streptomyces Sp. Strain F1, a Potential Source for Glycoside Hydrolases

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Draft Genome Sequence of Streptomyces Sp. Strain F1, a Potential Source for Glycoside Hydrolases BJM 224 1–3 ARTICLE IN PRESS b r a z i l i a n j o u r n a l o f m i c r o b i o l o g y x x x (2 0 1 7) xxx–xxx ht tp://www.bjmicrobiol.com.br/ 1 Genome Announcement 2 Draft genome sequence of Streptomyces sp. strain 3 F1, a potential source for glycoside hydrolases 4 isolated from Brazilian soil a,b,1 a,1 5 Q1 Ricardo Rodrigues de Melo , Gabriela Felix Persinoti , a a a,∗ 6 Douglas Antonio Alvaredo Paixão , Fábio Márcio Squina , Roberto Ruller , b,∗ 7 Helia Harumi Sato a 8 Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), 9 Campinas, São Paulo, Brazil b 10 Universidade Estadual de Campinas (UNICAMP), Faculdade de Engenharia de Alimentos, Departamento de Ciência de Alimentos, 11 Campinas, São Paulo, Brazil 12 a r a t b 13 i c l e i n f o s t r a c t 14 15 Article history: Here, we show the draft genome sequence of Streptomyces sp. F1, a strain isolated from 16 Received 26 September 2016 soil with great potential for secretion of hydrolytic enzymes used to deconstruct cellulosic 17 Accepted 22 November 2016 biomass. The draft genome assembly of Streptomyces sp. strain F1 has 87 contigs with a 18 Available online xxx total genome size of 8,162,446 bp and G + C 72.63%. Preliminary genome analysis identified 327 proteins as Carbohydrate-Active Enzymes, being 141 glycoside hydrolases organized in Associate Editor: John McCulloch 46 distinct families. This draft genome information provides new insights on the key genes 19 encoding hydrolytic enzymes involved in biomass deconstruction employed by soil bacteria. 20 Keywords: © 2017 Published by Elsevier Editora Ltda. on behalf of Sociedade Brasileira de 21 Actinobacteria Microbiologia. This is an open access article under the CC BY-NC-ND license (http:// 22 Glycoside hydrolases creativecommons.org/licenses/by-nc-nd/4.0/). 23 Streptomyces 24 Draft genome sequence 25 Soil bacteria of the Actinobacteria phylum. During their lifetime, these soil 30 Introduction bacteria are able to differentiate, produce aerial mycelia and 31 3 a wide variety of secondary metabolites. Although a large 32 26 Streptomyces species are aerobic Gram-positive bacteria best number of Streptomyces species can grow on plant biomass, 33 1 27 known industrially as producers of natural antibiotics, but understanding of key genes encoding hydrolytic enzymes 34 28 they are also recognized for their capacity to utilize cellulosic involved in biomass degrading by Streptomyces is currently 35 2 2,4–7 29 biomass. Phylogenetically, Streptomyces is the largest genus limited to a few soil-isolates. Streptomyces sp. strain F1 ∗ Corresponding authors. E-mails: [email protected] (R. Ruller), [email protected] (H.H. Sato). 1 These authors contributed equally to this work. http://dx.doi.org/10.1016/j.bjm.2016.11.010 1517-8382/© 2017 Published by Elsevier Editora Ltda. on behalf of Sociedade Brasileira de Microbiologia. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Please cite this article in press as: Melo RR, et al. Draft genome sequence of Streptomyces sp. strain F1, a potential source for glycoside hydrolases BJM 224 1–3 isolated from Brazilian soil. Braz J Microbiol. (2017), http://dx.doi.org/10.1016/j.bjm.2016.11.010 BJM 224 1–3 ARTICLE IN PRESS 2 b r a z i l i a n j o u r n a l o f m i c r o b i o l o g y x x x (2 0 1 7) xxx–xxx assembly provides a preliminary landscape of the genomic 84 Table 1 – Summary of genome features of Streptomyces and metabolic capabilities of Streptomyces sp. F1. 85 sp F1. Features Source Soil Nucleotide sequence accession number 86 Genome size, Mb 8.1 GC content % 0.73 The whole genome sequences of Streptomyces sp. F1 have been 87 tRNA 66 deposited at DDBJ/EMBL/GenBank under accession number 88 rRNA 9 FKJI00000000. 89 Protein coding sequences 7397 Conflict of interest 36 was isolated from soil containing decomposing organic matter 37 collected in Campinas, São Paulo, Brazil. This isolated strain The authors declare no conflicts of interest. 90 38 showed ability to grow in culture medium containing cellu- 39 lose or hemicellulose as sole carbon source, and to secrete 40 extracellular enzymes belonging to the glycoside hydrolases Acknowledgements 41 (GHs) families. Glycoside hydrolases are a group of enzymes 42 that play an important role in the conversion of lignocellulosic The authors gratefully acknowledge the Brazilian National Q2 91 43 biomass into small chemical building blocks, which can then Council for Scientific and Technological Development 92 44 be used to produce biofuels and other important intermedi- 8 (CNPq) for their financial support and fellowships, and 93 45 ary molecules. Here, we show the draft genome sequence of CNPEM-CTBE for the use of Sequencing and Robotics NGS 94 46 Streptomyces sp. F1, to identify GHs family members and to facility. 95 47 improve understanding of natural biomass utilization by soil 48 bacteria. 96 49 Genomic DNA extraction from Streptomyces sp. F1 was r e f e r e n c e s 50 carried out using FastDNA SPIN Kit for soil (MP Biomedi- 97 51 cals, Irvine, CA) according to the manufacturer’s instructions. 52 The genome was sequenced by whole genome shotgun 1. Barbe V, Bouzon M, Mangenot S, et al. Complete genome 98 53 sequencing using the Illumina HiSeq 2500 System at CTBE sequence of Streptomyces cattleya NRRL 8057, a producer of 99 54 Sequencing and Robotics NGS facility, generating 8,147,881 antibiotics and fluorometabolites. J Bacteriol. 100 × 55 paired end reads (2 100 bp). Reads were preprocessed with 2011;193(18):5055–5056. 101 9 56 Trimmomatic, to remove low-quality and adapter sequences 2. Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG. Aerobic 102 10 57 and were assembled using Spades version 3.6. The genome deconstruction of cellulosic biomass by an insect-associated 103 Streptomyces. Sci Rep. 2013;3:1030. 104 58 size was estimated to be 8,205,272, with approximately 100× 3. Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H. The complex 105 59 coverage. The draft genome assembly of Streptomyces sp. F1 extracellular biology of Streptomyces. FEMS Microbiol Rev. 106 60 has 87 contigs, 8,162,446 bp in length with G + C content of 2010;34(2):171–198. 107 61 72.63% (Table 1), an N50 of 259,843 bp, and the largest contig 4. Franco-Cirigliano MN, Rezende RDC, Gravina-Oliveira MP, 108 62 was 664,709 bp. Genome completeness was evaluated using et al. Streptomyces misionensis PESB-25 produces a 109 11 63 CheckM, which revealed that the assembly is 100% com- thermoacidophilic endoglucanase using sugarcane bagasse 110 111 64 plete, considering 460 marker genes from Streptomycetaceae and corn steep liquor as the sole organic substrates. Biomed Res Int. 2013;2013:1–10. 112 65 family. 5. Wibberg D, Al-Dilaimi A, Busche T, et al. Complete genome 113 66 Streptomyces sp. F1 showed highest 16S rDNA sequence sequence of Streptomyces reticuli, an efficient degrader of 114 67 similarity with Streptomyces misionensis strain JCM 4497. In crystalline cellulose. J Biotechnol Elsevier BV. 2016;222: 115 12 68 silico DNA–DNA hybridization (DDH) and Average Nucleotide 13–14. 116 13 69 Identity/Alignment fraction (gANI/AF) values of Streptomyces 6. Book AJ, Lewin GR, McDonald BR, et al. Cellulolytic 117 70 sp. F1 compared to Streptomyces misionensis DSM 40306, were Streptomyces strains associated with herbivorous insects 118 share a phylogenetically linked capacity to degrade 119 71 94.2% and 99.4%/0.99, respectively, suggesting that strain F1 lignocellulose. Appl Environ Microbiol. 2014;80(15): 120 72 may be classified as Streptomyces misionensis. 4692–4701. 121 73 Streptomyces sp. F1 genome was annotated using IMG- 7. Semêdo LTAS, Gomes RC, Linhares AA, et al. Streptomyces 122 74 JGI Microbial Genome Annotation Pipeline (img.jgi.doe.gov). drozdowiczii sp. nov., a novel cellulolytic streptomycete from 123 75 It has been predicted to include 7494 genes, being 7397 soil in Brazil. Int J Syst Evol Microbiol. 2004;54(4):1323–1328. 124 76 protein-coding genes, 9 rRNA (5S (6), 16S (1), 23S (2)), and 8. Horn S, Vaaje-Kolstad G, Westereng B, Eijsink VG. Novel 125 77 66 tRNA genes (Table 1). According to IMG functional anno- enzymes for the degradation of cellulose. Biotechnol Biofuels. 126 2012;5(1):45. 127 78 tation, 4453 genes were classified into COG categories, 5816 9. Bolger AM, Lohse M, Trimmomatic Usadel B. A flexible 128 79 in PFAM protein families, 1542 in TIGRFAM families, and 714 trimmer for Illumina Sequence Data. Bioinforma Adv. 129 80 in Transporter Classification. Further classification accord- 2014;30:2114. 130 81 ing to dbCAN showed that 327 proteins were classified as 10. Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome 131 82 Carbohydrate-Active Enzymes, being 141 glycoside hydro- assembly algorithm and its applications to single-cell 132 83 lases organized in 46 distinct families. The current genome sequencing. J Comput Biol. 2012;19(5):455–477. Please cite this article in press as: Melo RR, et al. Draft genome sequence of Streptomyces sp. strain F1, a potential source for glycoside hydrolases BJM 224 1–3 isolated from Brazilian soil. Braz J Microbiol. (2017), http://dx.doi.org/10.1016/j.bjm.2016.11.010 .
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