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Title: High-quality draft genome sequence of Flavobacterium suncheonense GH29-5 T (DSM 17707 T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5 T

Abstract

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5 T (DSM 17707 T ) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5 T is part of the Genomic Encyclopedia of Bacteria and Archaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5 T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5 T . Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5 T feeds rather on proteins than saccharides and lipids.

Authors:
 [1];  [1];  [1];  [2];  [2];  [2];  [3];  [4];  [4];  [5];  [6];  [7];  [6];  [6];  [6];  [6];  [7];  [6];  [2];  [8] more »;  [9];  [2] « less
  1. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
  2. Leibniz Inst. of Microorganisms and Cell Cultures, Braunschweig (Germany)
  3. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  4. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences, Center for Nanotechnology
  5. St. Petersburg State Univ. (Russia). Centre for Algorithmic Biotechnology
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  8. Newcastle Univ., Tyne (United Kingdom). School of Biology
  9. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379401
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Aerobic; Gliding motility; Greenhouse soil; Flavobacteriaceae; Bacteroidetes; GEBA; KMG-1; Tree of Life; GGDC; Carbohydrate active enzyme; Polysaccharide utilization loci

Citation Formats

Tashkandy, Nisreen, Sabban, Sari, Fakieh, Mohammad, Meier-Kolthoff, Jan P., Huang, Sixing, Tindall, Brian J., Rohde, Manfred, Baeshen, Mohammed N., Baeshen, Nabih A., Lapidus, Alla, Copeland, Alex, Pillay, Manoj, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C., and Hahnke, Richard L. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T. United States: N. p., 2016. Web. doi:10.1186/s40793-016-0159-5.
Tashkandy, Nisreen, Sabban, Sari, Fakieh, Mohammad, Meier-Kolthoff, Jan P., Huang, Sixing, Tindall, Brian J., Rohde, Manfred, Baeshen, Mohammed N., Baeshen, Nabih A., Lapidus, Alla, Copeland, Alex, Pillay, Manoj, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C., & Hahnke, Richard L. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T. United States. doi:10.1186/s40793-016-0159-5.
Tashkandy, Nisreen, Sabban, Sari, Fakieh, Mohammad, Meier-Kolthoff, Jan P., Huang, Sixing, Tindall, Brian J., Rohde, Manfred, Baeshen, Mohammed N., Baeshen, Nabih A., Lapidus, Alla, Copeland, Alex, Pillay, Manoj, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C., and Hahnke, Richard L. Thu . "High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T". United States. doi:10.1186/s40793-016-0159-5. https://www.osti.gov/servlets/purl/1379401.
@article{osti_1379401,
title = {High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T},
author = {Tashkandy, Nisreen and Sabban, Sari and Fakieh, Mohammad and Meier-Kolthoff, Jan P. and Huang, Sixing and Tindall, Brian J. and Rohde, Manfred and Baeshen, Mohammed N. and Baeshen, Nabih A. and Lapidus, Alla and Copeland, Alex and Pillay, Manoj and Reddy, T. B. K. and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia and Markowitz, Victor and Woyke, Tanja and Göker, Markus and Klenk, Hans-Peter and Kyrpides, Nikos C. and Hahnke, Richard L.},
abstractNote = {Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5 T (DSM 17707 T ) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5 T is part of the Genomic Encyclopedia of Bacteria and Archaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5 T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5 T . Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5 T feeds rather on proteins than saccharides and lipids.},
doi = {10.1186/s40793-016-0159-5},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United States},
year = {2016},
month = {6}
}

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Figures / Tables:

Fig. 1 Fig. 1 : Phylogenetic tree of the genus Flavobacterium and its most closely related genus Capnocytophaga. Modified from Hahnke et al. [68]. In short: the tree was inferred from 1254 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion. The branches are scaled in termsmore » of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1000 ML bootstrap replicates (left) and from 1000 maximum-parsimony bootstrap replicates (right) if larger than 60 %« less

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