PROKARYOTES
crossm Draft Genome Sequence of Listeria monocytogenes Strain ATCC 7644 Marc-Olivier Duceppe,a Catherine Carrillo,b Hongsheng Huanga Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield, Ontario, Canadaa; Canadian Food Inspection Agency, Ottawa Laboratory Carling, Ontario, Canadab
Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an important foodborne bacterial pathogen for humans worldwide with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection).
ABSTRACT
L
isteria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium and an important foodborne bacterial pathogen for humans worldwide with high mortality rates (1). Listeria species have been widely used in numerous research studies for biology, pathogenesis, and diagnostics (2). In particular, L. monocytogenes strain ATCC 7644 has been used frequently as a model organism (3, 4), but its whole-genome sequence is not available, which limits the understanding of its molecular pathogenesis. Therefore, this article reports its draft genome sequence. L. monocytogenes strain ATCC 7644 (serogroup 1/2c) isolated from a human was obtained from ATCC (ATCC, Manassas, VA, USA) and stored at ⫺80°C. Genomic DNA was isolated from overnight cultures grown at 37°C on brain and heart infusion agar using the Qiagen DNeasy blood and tissue DNA purification kit (product no. 69504, Qiagen, Toronto, Ontario, Canada). Three sequencing libraries were constructed from three independent cultures/DNA extractions using the Nextera XT DNA sample preparation kit (Illumina, Inc., San Diego, CA), and library quality was analyzed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with the Illumina MiSeq platform (Illumina, Inc.) using v3 reagent kits. A total of 2,889,385 300-bp paired-end reads were generated. Sequencing adapter and low-quality bases were trimmed (bbduk), and overlapping pairs were merged (bbmerge) using the bbtools software suite (http://jgi.doe.gov/data -and-tools/bbtools/). Preprocessed reads were assembled using SPAdes v3.10.1 (5) and polished with Pilon v1.22 (6). Assembly resulted in 11 contigs (⬎1,000 bp), with an average of 580-fold genome coverage. Contigs were ordered with Mauve v2015-02-13 using GenBank accession no. NC_018588 as reference, the closest genome to L. monocytogenes ATCC 7644 from RefSeq, according to Mash v1.1.1 (7). The combined length of the draft genome was 2,964,284 bp, with a G⫹C content of 37.83%. Gene predictions and annotations were performed using the NCBI Prokaryotic Genome Annotation Pipeline (8), which predicted 3,033 genes, 2,967 coding sequences (CDS), 8 rRNAs, and 54 tRNAs. Two prophage sequences of 57.4 kb and 10 kb, respectively, were detected by PHASTER (9). Two of the 11 contigs were matching plasmid sequences. Accession number(s). This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. NGZM00000000. The version described in this paper is the first version, NGZM01000000.
Received 11 August 2017 Accepted 18 August 2017 Published 21 September 2017 Citation Duceppe M-O, Carrillo C, Huang H. 2017. Draft genome sequence of Listeria monocytogenes strain ATCC 7644. Genome Announc 5:e00970-17. https://doi.org/10.1128/ genomeA.00970-17. © Crown copyright 2017. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Marc-Olivier Duceppe, [email protected], or Catherine Carrillo, [email protected].
ACKNOWLEDGMENTS We thank Beverley Phipps-Todd and Paul Manninger (OLC) for providing technical assistance. This work was funded by the Canadian Food Inspection Agency. Volume 5 Issue 38 e00970-17
genomea.asm.org 1
Duceppe et al.
REFERENCES 1. de Noordhout CM, Devleesschauwer B, Angulo FJ, Verbeke G, Haagsma J, Kirk M, Havelaar A, Speybroeck N. 2014. The global burden of listeriosis: a systematic review and meta-analysis. Lancet Infect Dis 14:1073–1082. https://doi.org/10.1016/S1473-3099(14)70870-9. 2. Hamon M, Bierne H, Cossart P. 2006. Listeria monocytogenes: a multifaceted model. Nat Rev Microbiol 4:423– 434. https://doi.org/10.1038/ nrmicro1413. 3. Longhi C, Maffeo A, Penta M, Petrone G, Seganti L, Conte MP. 2003. Detection of Listeria monocytogenes in Italian-style soft cheeses. J Appl Microbiol 94:879 – 885. https://doi.org/10.1046/j.1365-2672.2003.01921.x. 4. Rocha CE, Mol JPS, Garcia LNN, Costa LF, Santos RL, Paixão TA. 2017. Comparative experimental infection of Listeria monocytogenes and Listeria ivanovii in bovine trophoblasts. PLoS One 12:e0176911. https://doi.org/ 10.1371/journal.pone.0176911. 5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-
Volume 5 Issue 38 e00970-17
6.
7.
8.
9.
sembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. https://doi.org/10.1371/journal.pone.0112963. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17:132. https://doi.org/10.1186/ s13059-016-0997-x. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi .org/10.1093/nar/gkw569. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16 –W21. https://doi.org/10.1093/nar/gkw387.
genomea.asm.org 2
crossm Draft Genome Sequence of Listeria monocytogenes Strain ATCC 7644 Marc-Olivier Duceppe,a Catherine Carrillo,b Hongsheng Huanga Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield, Ontario, Canadaa; Canadian Food Inspection Agency, Ottawa Laboratory Carling, Ontario, Canadab
Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an important foodborne bacterial pathogen for humans worldwide with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection).
ABSTRACT
L
isteria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium and an important foodborne bacterial pathogen for humans worldwide with high mortality rates (1). Listeria species have been widely used in numerous research studies for biology, pathogenesis, and diagnostics (2). In particular, L. monocytogenes strain ATCC 7644 has been used frequently as a model organism (3, 4), but its whole-genome sequence is not available, which limits the understanding of its molecular pathogenesis. Therefore, this article reports its draft genome sequence. L. monocytogenes strain ATCC 7644 (serogroup 1/2c) isolated from a human was obtained from ATCC (ATCC, Manassas, VA, USA) and stored at ⫺80°C. Genomic DNA was isolated from overnight cultures grown at 37°C on brain and heart infusion agar using the Qiagen DNeasy blood and tissue DNA purification kit (product no. 69504, Qiagen, Toronto, Ontario, Canada). Three sequencing libraries were constructed from three independent cultures/DNA extractions using the Nextera XT DNA sample preparation kit (Illumina, Inc., San Diego, CA), and library quality was analyzed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with the Illumina MiSeq platform (Illumina, Inc.) using v3 reagent kits. A total of 2,889,385 300-bp paired-end reads were generated. Sequencing adapter and low-quality bases were trimmed (bbduk), and overlapping pairs were merged (bbmerge) using the bbtools software suite (http://jgi.doe.gov/data -and-tools/bbtools/). Preprocessed reads were assembled using SPAdes v3.10.1 (5) and polished with Pilon v1.22 (6). Assembly resulted in 11 contigs (⬎1,000 bp), with an average of 580-fold genome coverage. Contigs were ordered with Mauve v2015-02-13 using GenBank accession no. NC_018588 as reference, the closest genome to L. monocytogenes ATCC 7644 from RefSeq, according to Mash v1.1.1 (7). The combined length of the draft genome was 2,964,284 bp, with a G⫹C content of 37.83%. Gene predictions and annotations were performed using the NCBI Prokaryotic Genome Annotation Pipeline (8), which predicted 3,033 genes, 2,967 coding sequences (CDS), 8 rRNAs, and 54 tRNAs. Two prophage sequences of 57.4 kb and 10 kb, respectively, were detected by PHASTER (9). Two of the 11 contigs were matching plasmid sequences. Accession number(s). This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. NGZM00000000. The version described in this paper is the first version, NGZM01000000.
Received 11 August 2017 Accepted 18 August 2017 Published 21 September 2017 Citation Duceppe M-O, Carrillo C, Huang H. 2017. Draft genome sequence of Listeria monocytogenes strain ATCC 7644. Genome Announc 5:e00970-17. https://doi.org/10.1128/ genomeA.00970-17. © Crown copyright 2017. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Marc-Olivier Duceppe, [email protected], or Catherine Carrillo, [email protected].
ACKNOWLEDGMENTS We thank Beverley Phipps-Todd and Paul Manninger (OLC) for providing technical assistance. This work was funded by the Canadian Food Inspection Agency. Volume 5 Issue 38 e00970-17
genomea.asm.org 1
Duceppe et al.
REFERENCES 1. de Noordhout CM, Devleesschauwer B, Angulo FJ, Verbeke G, Haagsma J, Kirk M, Havelaar A, Speybroeck N. 2014. The global burden of listeriosis: a systematic review and meta-analysis. Lancet Infect Dis 14:1073–1082. https://doi.org/10.1016/S1473-3099(14)70870-9. 2. Hamon M, Bierne H, Cossart P. 2006. Listeria monocytogenes: a multifaceted model. Nat Rev Microbiol 4:423– 434. https://doi.org/10.1038/ nrmicro1413. 3. Longhi C, Maffeo A, Penta M, Petrone G, Seganti L, Conte MP. 2003. Detection of Listeria monocytogenes in Italian-style soft cheeses. J Appl Microbiol 94:879 – 885. https://doi.org/10.1046/j.1365-2672.2003.01921.x. 4. Rocha CE, Mol JPS, Garcia LNN, Costa LF, Santos RL, Paixão TA. 2017. Comparative experimental infection of Listeria monocytogenes and Listeria ivanovii in bovine trophoblasts. PLoS One 12:e0176911. https://doi.org/ 10.1371/journal.pone.0176911. 5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-
Volume 5 Issue 38 e00970-17
6.
7.
8.
9.
sembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. https://doi.org/10.1371/journal.pone.0112963. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17:132. https://doi.org/10.1186/ s13059-016-0997-x. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi .org/10.1093/nar/gkw569. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16 –W21. https://doi.org/10.1093/nar/gkw387.
genomea.asm.org 2
