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
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:
- more »
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618968
- Alternate Identifier(s):
- OSTI ID: 1379401
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- 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 Kingdom: 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 Kingdom. https://doi.org/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 Kingdom. https://doi.org/10.1186/s40793-016-0159-5.
@article{osti_1618968,
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 Kingdom},
year = {Thu Jun 16 00:00:00 EDT 2016},
month = {Thu Jun 16 00:00:00 EDT 2016}
}
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https://doi.org/10.1186/s40793-016-0159-5
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Figures / Tables:
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 »
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