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Title: Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7

Abstract

Here, we and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Authors:
 [1];  [2];  [3];  [3];  [4];  [4];  [5]; ORCiD logo [4];  [6];  [7];  [7];  [7];  [7];  [7];  [7];  [7];  [7];  [7];  [7];  [7] more »;  [7];  [7];  [7];  [7];  [8] « less
  1. Univ. of Tennessee, Knoxville, TN (United States)
  2. The Weismann Institute of Science, Rehovot (Israel)
  3. Tel-Aviv Univ., Ramat Aviv (Israel)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); BioEnergy Science Center, Oak Ridge, TN (United States)
  6. Univ. of Oklahoma, Norman, OK (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); BioEnergy Science Center, Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1327678
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Genome Announcements
Additional Journal Information:
Journal Volume: 4; Journal Issue: 5; Journal ID: ISSN 2169-8287
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Utturkar, Sagar M., Bayer, Edward A., Borovok, Ilya, Lamed, Raphael, Hurt, Richard A., Land, Miriam L., Klingeman, Dawn M., Elias, Dwayne, Zhou, Jizhong, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, and Brown, Steven D.. Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7. United States: N. p., 2016. Web. doi:10.1128/genomeA.01043-16.
Utturkar, Sagar M., Bayer, Edward A., Borovok, Ilya, Lamed, Raphael, Hurt, Richard A., Land, Miriam L., Klingeman, Dawn M., Elias, Dwayne, Zhou, Jizhong, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, & Brown, Steven D.. Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7. United States. doi:10.1128/genomeA.01043-16.
Utturkar, Sagar M., Bayer, Edward A., Borovok, Ilya, Lamed, Raphael, Hurt, Richard A., Land, Miriam L., Klingeman, Dawn M., Elias, Dwayne, Zhou, Jizhong, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, and Brown, Steven D.. 2016. "Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7". United States. doi:10.1128/genomeA.01043-16. https://www.osti.gov/servlets/purl/1327678.
@article{osti_1327678,
title = {Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7},
author = {Utturkar, Sagar M. and Bayer, Edward A. and Borovok, Ilya and Lamed, Raphael and Hurt, Richard A. and Land, Miriam L. and Klingeman, Dawn M. and Elias, Dwayne and Zhou, Jizhong and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Palaniappan, Krishnaveni and Varghese, Neha and Mikhailova, Natalia and Stamatis, Dimitrios and Reddy, T. B. K. and Ngan, Chew Yee and Daum, Chris and Shapiro, Nicole and Markowitz, Victor and Ivanova, Natalia and Kyrpides, Nikos and Woyke, Tanja and Brown, Steven D.},
abstractNote = {Here, we and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.},
doi = {10.1128/genomeA.01043-16},
journal = {Genome Announcements},
number = 5,
volume = 4,
place = {United States},
year = 2016,
month = 9
}

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  • We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes forClostridium thermocellumAD2,Clostridium thermocellumLQRI, andPelosinus fermentansR7.
  • The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Finally, nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.
  • The crude extracellular cellulase of Clostridium thermocellum LQRI (virgin strain) was very active and solubilized microcrystalline cellulose at one-half the rate observed for the extracellular cellulase of Trichoderma reesei QM9414 (mutant strain). Clostridium thermocellum cellulase activity differed considerably from that of Trichoderma reesei as follows: higher endoglucanase/exoglucanase activity ratio; absence of extracellular cellobiase or beta-xylosidase activity; long-chain oligosaccharides instead of short-chain oligosaccharides as initial (15-min) hydrolytic products on microcrystalline cellulose; mainly cellobiose or xylobiose as long-term (24-h) hydrolysis products of Avicel and MN300 or xylan; and high activity and stability at 60 to 70 degrees Celcius. Under optimized reaction conditions,more » the kinetic properties (V max, 0.4 mu mol/min per mg of protein; energy of activation, 33 kJ; temperature coefficient, 1.8) of Clostridium thermocellum cellulose-solubilizing activity were comparable to those reported for Trichoderma reesei, except that the dyed Avicel concentration at half-maximal velocity was twofold higher (182 mu M). The cellulose-solubilizing activity of the two crude cellulases differed considerably in response to various enzyme inhibitors. Most notably, Ag/sup 2 +/ and Hg/sup 2 +/ effectively inhibited Clostridium thermocellum but not Trichoderma reesei cellulase at less than 20 mu M, whereas Ca/sup 2 +/, Mg/sup 2 +/, and Mn/sup 2 +/ inhibited Trichoderma reesei but not Clostridium thermocellum cellulase at greater than 10 mM. Both enzymes were inhibited by Cu/sup 2 +/ (greater than 20 mM), Zn2+ (greater than 10 mM), and ethylene glycol-bis (beta-aminoethyl ether)-N, N-tetraacetic acid (greater than 10 mM). The overal rates of cellooligosaccharide degradation were higher for Trichoderma reesei than for Clostridium thermocellum cellulase, except that the rates of conversion of cellohexaose to cellotrisse were equivalent.« less
  • Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.