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. 2010 Oct 1;192(24):6494–6496. doi: 10.1128/JB.01064-10

Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production

Christopher L Hemme 1,2, Housna Mouttaki 1,2,3, Yong-Jin Lee 1,2, Gengxin Zhang 14, Lynne Goodwin 5, Susan Lucas 4, Alex Copeland 4, Alla Lapidus 4, Tijana Glavina del Rio 4, Hope Tice 4, Elizabeth Saunders 5, Thomas Brettin 5,6, John C Detter 5, Cliff S Han 5, Sam Pitluck 4, Miriam L Land 6, Loren J Hauser 6, Nikos Kyrpides 4, Natalia Mikhailova 4, Zhili He 1,2, Liyou Wu 1,2, Joy D Van Nostrand 1,2, Bernard Henrissat 7, Qiang He 8, Paul A Lawson 1, Ralph S Tanner 1, Lee R Lynd 9, Juergen Wiegel 10, Matthew W Fields 11, Adam P Arkin 12, Christopher W Schadt 13, Bradley S Stevenson 1, Michael J McInerney 1, Yunfeng Yang 13, Hailiang Dong 14, Defeng Xing 15, Nanqi Ren 15, Aijie Wang 15, Raymond L Huhnke 16, Jonathan R Mielenz 17, Shi-You Ding 18, Michael E Himmel 18, Safiyh Taghavi 19, Daniël van der Lelie 19, Edward M Rubin 4, Jizhong Zhou 1,2,*
PMCID: PMC3008519  PMID: 20889752

Abstract

Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae. Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.


Clostridial genomes were sequenced using a combination of Sanger (3× coverage, 8 kb, pMCL200), 454 (20× coverage), and Solexa methods. Standard sequencing protocols are listed on the Joint Genome Institute (JGI) website (http://www.jgi.doe.gov/sequencing/protocols/prots_production.html). Sanger and 454 reads were assembled as previously described (5). Automatic annotations were conducted for all draft genomes using the JGI-Oak Ridge National Laboratory (ORNL) annotation pipeline, and all draft genomes and annotations were loaded into the JGI Integrated Microbial Resource (IMG) for analysis (11). Due to difficulties in assembling and finishing low-GC, high-repeat genomes, many of the genomes targeted for sequencing could not be finished and are presented as a highquality permanent draft. Sequences available at the time of this analysis are listed in Table 1 and are categorized based on the latest Bergey's taxonomy (9).

TABLE 1.

Clostridium genome sequencing projects related to biomass conversion and biofuels production

Organism name Reference(s) Genome analysis
Accession no.c
Seq. statusa Size (Mb) No. of contigs % GC CDSb
Clostridium sensu stricto
    Clostridium cellulovorans 743B 17 F 5.2 1 31.2 4,256 CP002160
    Clostridium carboxidivorans P7 3, 8 PD 5.5 50 29.7 5,462 ACVI00000000
    Clostridium ragsdalei P11 3 P
Ruminococcaceae
    Acetivibrio cellulolyticus CD2 14 D 6.1 193 35.5 5,146 AEDB00000000
    Clostridium cellulolyticum H10 15 F 4.1 1 37.0 3,390 CP001348
    Clostridium papyrosolvens DSM 2782 10 PD 4.8 31 36.9 4,425 ACXX00000000
    Clostridium thermocellum JW20 DSM 4150 2 PD 3.8 26 39.0 3,077 ABVG00000000
    Clostridium thermocellum LQRI DSM 2360 12 PD 3.5 23 39.1 2,914 ACVX00000000
Thermoanaerobacteraceae
    Thermoanaerobacter wiegelii Rt8.B1 1 D 2.7 169 34.2 2,906 Pending
    Thermoanaerobacter brockii sp. finnii Ako-1 7, 21 PD 2.2 85 34.3 2,279 ACQZ00000000
    Thermoanaerobacter sp. CCSD1 22 PD 2.2 18 34.3 2,146 ACXY00000000
    Thermoanaerobacter sp. X513 16 F 2.3 1 34.5 2,330 ACPF00000000
    Thermoanaerobacter sp. X561 16 PD 2.4 8 34.5 2,332 ACXP00000000
    Thermoanaerobacter pseudethanolicus 39E 13 F 2.4 1 34.0 2,243 CP000924
    Thermoanaerobacter sp. X514 16 F 2.5 1 34.0 2,349 CP000923
    Thermoanaerobacter italicus Ab9 4 F 2.4 1 34.1 2,271 CP001936
    Thermoanaerobacter mathranii subsp. mathranii A3 DSM 11426 6 F 2.3 1 34.3 2,161 CP002032
    Thermoanaerobacter ethanolicus JW200 19 D 2.2 376 34.0 2423 ACXY00000000
    Thermoanaerobacter siderophilus L-64 18 P
    Thermoanaerobacterium thermosaccharolyticum DSM 571 7 F 2.7 1 34.1 2,161 CP002171
    Thermoanaerobacterium xylanolyticum LX11 7 D 2.5 91 34.8 2,509 Pending
Miscellaneous
    Clostridium saccharolyticum DSM 2544 7 F 4.6 1 45.0 4,160 CP002109
    Ethanoligenens harbinense YUAN-3 20 D 3.0 3 55.5 2,787 ADJQ00000000
a

Sequencing status: F, finished; PD, permanent high-quality draft; D, draft (ongoing); P, sequence pending.

b

No. of annotated protein coding sequences.

c

GenBank accession number.

Acknowledgments

The biomass-converting clostridium sequencing project was initiated by the Clostridium Sequencing Consortium (see author list) through the Joint Genome Institute. The genome sequencing work was performed under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory, under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory, under contract no. DE-AC52-07NA27344, Los Alamos National Laboratory, under contract no. DE-AC02-06NA25396, and Oak Ridge National Laboratory, under contract no. DE-AC05-00OR22725. This work was supported by NSF-EPSC.R grant 105118300.

Footnotes

Published ahead of print on 1 October 2010.

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