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Title: Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds

Abstract

Jiangella gansuensis strain YIM 002 T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.

Authors:
 [1];  [2];  [1];  [3];  [1];  [4];  [5];  [6];  [6];  [6];  [6];  [6];  [7];  [8];  [9];  [6];  [10];  [11];  [12]
  1. Sun Yat-Sen Univ., Guangzhou, (China). College of Life Science
  2. Newcastle Univ., Tyne (United Kingdom). School of Biology
  3. Chinese Academy of Sciences (CAS), Beijing (China). Key Lab. of Tropical Plant Resources and Sustainable Use
  4. King Saud Univ., Riyadh (Saudi Arabia). Bioproducts Research Chair; Beni-Suef Univ. (Egypt). Botany and Microbiology Dept.
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); St. Petersburg State Univ. (Russia). Center for Algorithmic Biotechnology
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Leibniz Inst. for German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig (Germany)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  9. Univ. of California, Davis, CA (United States)
  10. Leibniz Inst. for German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig (Germany); Newcastle Univ., Tyne (United Kingdom). School of Biology
  11. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Bilogical Sciences
  12. Sun Yat-Sen Univ., Guangzhou, (China). College of Life Science; Chinese Academy of Sciences (CAS), Beijing (China). Xinjiang Inst. of Ecology and Geography
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:
1379721
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; jiangella gansuensis; jiangellales; desert; genome; taxonomic comments; GEBA

Citation Formats

Jiao, Jian-Yu, Carro, Lorena, Liu, Lan, Gao, Xiao-Yang, Zhang, Xiao-Tong, Hozzein, Wael N., Lapidus, Alla, Huntemann, Marcel, Reddy, T. B. K., Varghese, Neha, Hadjithomas, Michalis, Ivanova, Natalia N., Göker, Markus, Pillay, Manoj, Eisen, Jonathan A., Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0226-6.
Jiao, Jian-Yu, Carro, Lorena, Liu, Lan, Gao, Xiao-Yang, Zhang, Xiao-Tong, Hozzein, Wael N., Lapidus, Alla, Huntemann, Marcel, Reddy, T. B. K., Varghese, Neha, Hadjithomas, Michalis, Ivanova, Natalia N., Göker, Markus, Pillay, Manoj, Eisen, Jonathan A., Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., & Li, Wen-Jun. Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. United States. doi:10.1186/s40793-017-0226-6.
Jiao, Jian-Yu, Carro, Lorena, Liu, Lan, Gao, Xiao-Yang, Zhang, Xiao-Tong, Hozzein, Wael N., Lapidus, Alla, Huntemann, Marcel, Reddy, T. B. K., Varghese, Neha, Hadjithomas, Michalis, Ivanova, Natalia N., Göker, Markus, Pillay, Manoj, Eisen, Jonathan A., Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Li, Wen-Jun. Fri . "Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds". United States. doi:10.1186/s40793-017-0226-6. https://www.osti.gov/servlets/purl/1379721.
@article{osti_1379721,
title = {Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds},
author = {Jiao, Jian-Yu and Carro, Lorena and Liu, Lan and Gao, Xiao-Yang and Zhang, Xiao-Tong and Hozzein, Wael N. and Lapidus, Alla and Huntemann, Marcel and Reddy, T. B. K. and Varghese, Neha and Hadjithomas, Michalis and Ivanova, Natalia N. and Göker, Markus and Pillay, Manoj and Eisen, Jonathan A. and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Li, Wen-Jun},
abstractNote = {Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.},
doi = {10.1186/s40793-017-0226-6},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {2017},
month = {2}
}

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Figures / Tables:

Figure 1 Figure 1: Scanning electron micrograph of Jiangella gansuensis strain YIM 002T grown on ISP medium 2 for 14d at 28 °C. Bar size: 2 μm

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    Works referencing / citing this record:

    Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds [Supplemental Data]
    dataset, February 2017

    • Jiao, Jian-Yu; Carro, Lorena; Liu, Lan
    • figshare-Supplementary information for journal article at DOI: 10.1186/s40793-017-0226-6, 1 PDF file (92.27 kB); 1 DOCX file (73.46 kB)
    • DOI: 10.6084/m9.figshare.c.3683143

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.