Reannotation of the genome sequence of Clostridium

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A regular update of genome annotations is a prerequisite step to help maintain the accuracy and relevance .... In addition the locus tag prefix must be separated from the tag value .... (clustered regularly interspaced short palindromic repeats).
%paper no. jmm030452 charlesworth ref: jmm030452&

Clostridium difficile

Journal of Medical Microbiology (2011), 60, 000–000

DOI 10.1099/jmm.0.030452-0

Reannotation of the genome sequence of Clostridium difficile strain 630 Marc Monot,1 Caroline Boursaux-Eude,2 Marie Thibonnier,1 David Vallenet,3 Ivan Moszer,2 Claudine Medigue,3 Isabelle Martin-Verstraete1,4 and Bruno Dupuy1 1

Correspondence

Laboratoire Pathogene`se des Bacte´ries Anae´robies, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France

Marc Monot [email protected]

2

Inte´gration et Analyse Ge´nomiques, Institut Pasteur, 28 Rue du Dr Roux, F-75724 Paris Cedex 15, France

3

CNRS UMR 8030, Universite´ d’Evry & CEA, IG, Genoscope – LABGeM, 2 Rue Gaston Cre´mieux, CP 5706, F-91057 Evry Cedex, France

4

Universite´ Paris Diderot-Paris 7, 7 Boulevard Diderot, F-75012 Paris, France




Special thanks to Mohamed Sebaihia (Sanger Institute, Cambridge, UK) who allowed us to update the original database entry (AM180355). We thank Richard Stabler (London School of Hygiene and Tropical Medicine, London, UK) who gave several comparison gene files between the reference genome and 027 strains. Special thanks to Ana Antunes, Sylvie Bouttier, Thomas Candela, Claire Janoir and Johann Peltier who provided help with specific gene annotations. We are grateful to Marc Griffiths and Erica Porter for their help with English corrections. B. D., M. M., C. B.-E. and I. M. designed the study. C. B.-E. and M. M. carried out the major part of the manual reannotation of the genome together with M. T., and I. M.-V. D. V. and C. M. were involved in automatic reannotation and administration of the MicroScope platform. M. M., I. M.-V. and B. D. wrote the manuscript.

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Comparative genome and phenotypic analysis of Clostridium difficile

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Dear Authors, Please find enclosed a proof of your article for checking. When reading through your proof, please check carefully authors’ names, scientific data, data in tables, any mathematics and the accuracy of references. Please do not make any unnecessary changes at this stage. All necessary corrections should be marked on the proof at the place where the correction is to be made; please write the correction clearly in the margin (if in the text they may be overlooked). Any queries that have arisen during preparation of your paper for publication are listed below and indicated on the proof. Please provide your answers when returning your proof. Please return your proof by Fax (+44 (0)118 988 1834) within 2 days of receipt.

Query no.

Query

1

’HAMAP’ has been defined as ’high-quality automated and manual annotation of microbial proteomes’. Is this definition correct?

2

’INSDC’ has been defined as ’international nucleotide sequence database collection’. Is this definition correct?

3

‘Sanger Institute’ has been added as the institute for ‘Mohamed Sebaihia’. Is this institute correct?(b) ‘London School of Hygiene and Tropical Medicine’ has been added as the institute for ‘Richard Stabler’. Is this institute correct?

4

Please would you provide the institute/university names with city and country for the following people : ?Ana Antunes/ Sylvie Bouttier/ Thomas Candela/ Claire Janoir/ Johann Peltier/ Marc Griffiths/ Erica Porter ? ?

5

For the entry ‘CD630_30130/CD630_30140/CD630_3015’ the locus tag ‘CD630_3015’ has been changed to ‘CD630_30150’. Is this change correct?

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