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
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