# Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes

Valentin Loux, Gwendoline Coeuret, Monique Zagorec, Marie-Christine Champomier-Verges, Stephane Chaillou

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Valentin Loux, Gwendoline Coeuret, Monique Zagorec, Marie-Christine Champomier-Verges, Stephane Chaillou. Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes. Genome Announcements, 2018, 6 (16), 3 p. 10.1128/genomeA.00082-18. hal-02619093

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# Complete and Draft Genome Sequences of Nine *Lactobacillus sakei* Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes

Valentin Loux,ᵇ Gwendoline Coeuret,ª Monique Zagorec,ª* Marie-Christine Champomier Vergès,ª Stéphane Chaillouª

**ABSTRACT** We present here the complete and draft genome sequences of nine *Lactobacillus sakei* strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important food-borne species.

Lactobacillus sakei is a highly prevalent species found in meat and seafood products. It is used as a model organism for studying food fermentation, biopreservation, and spoilage. These different outcomes might depend on the food matrix and storage conditions but can also be strain dependent, as the species is known to exhibit high intraspecies diversity (1, 2).

Therefore, sequencing of the *L. sakei* genome was carried out to obtain at least two complete genome sequences from strains belonging to each of the three lineages previously shown by multilocus sequence typing (2). The remaining strains were sequenced as drafts. Furthermore, two complete large plasmids were fully sequenced to increase our knowledge of the plasmidic repertoire of the species, including the 70-kb plasmid pJ23A1 of the parent strain, *L. sakei* 23K (3).

The whole-genome sequencing of these strains was carried out by Eurofins MWG Operon Laboratories (Ebersberg, Germany) using either a mix of Sanger and pyrosequencing GS-FLX+ for complete genomes or Illumina MiSeq 2 × 150-bp paired-end libraries for draft genomes. Reads were assembled de novo by Velvet software (4). All contigs were aligned against the relevant 23K strain complete genome using progressiveMauve (5), and annotation was performed with a combination of MicroScope (6) and AGMIAL (7) platforms.

**Accession number(s).** Sequence data have been deposited in DDBJ/ENA/GenBank under the accession numbers cited in Table 1.

## ACKNOWLEDGMENTS

This work was conducted in the framework of the INRA COMETES (Controlling Meat Ecosystems) project from the Meta-omics and Microbial Ecosystems (MEM) metaprogramme. We are also grateful to the INRA MIGALE bioinformatics platform (http://migale.jouy.inra.fr) for providing computational resources and data storage.

The LABGeM (CEA/IG/Genoscope and CNRS UMR8030) and the France Génomique National Infrastructure (funded as part of the Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contract ANR-10-INBS-09) are acknowledged for support within the MicroScope annotation platform.

Received 22 January 2018 Accepted 19

March 2018 Published 19 April 2018

**Citation** Loux V, Coeuret G, Zagorec M, Champomier Vergès M-C, Chaillou S. 2018. Complete and draft genome sequences of nine *Lactobacillus sakei* strains selected from the three known phylogenetic lineages and their main clonal complexes. Genome Announc 6:e00082-18. https://doi.org/10.1128/genomeA.00082-18.

**Copyright** © 2018 Loux et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Stéphane Chaillou, stephane.chaillou@inra.fr.

* Present address: Monique Zagorec, SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France.

<footnote>ªMICALIS institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France</footnote>

<footnote>ᵇMalAGE, Mathématiques et Informatique Appliquées du Génome à l'Environnement, INRA, Université Paris-Saclay, Jouy-en-Josas, France</footnote>
<table><caption>TABLE 1 Overview of the complete and draft genome assemblies from nine L. sakei strains</caption><thead><tr><th>Phylogeny</th><th>Status</th><th>Original strain name (synonyms)</th><th>Collection name</th><th>Source, yr</th><th>Genetic element</th><th>No. of contigs</th><th>Size (bp)</th><th>Coverage (x)</th><th>No. of CDSs</th><th>BioProject no.</th><th>GenBank accession no.</th></tr></thead><tbody><tr><td rowspan="2">Lineage 1<sup>a</sup></td><td rowspan="2">CC1A</td><td>Complete</td><td>J64 (64, JOUY-64)</td><td>CNCM I-4394</td><td>Dry sausage, 1982</td><td>1</td><td>2,050,232</td><td>49</td><td>2,102</td><td>PRJEB22335</td><td>LT960781</td></tr><tr><td>Complete</td><td>MFPB16A1401</td><td>CIP 110933</td><td>Beef carpaccio, 2009</td><td>1</td><td>46,347</td><td>65</td><td>55</td><td>PRJEB22335</td><td>LT960782</td></tr><tr><td rowspan="2">Lineage 2</td><td rowspan="2">CC2A</td><td>Complete</td><td>23K<sup>b</sup></td><td>CNCM I-4396</td><td>Dry sausage, 1990</td><td>1</td><td>1,994,583</td><td>51</td><td>1,960</td><td>PRJEB22338</td><td>LT960788</td></tr><tr><td>Complete</td><td>MFPB19A1501 (MFPB19)</td><td>CNCM I-4396</td><td>Beef carpaccio, 2009</td><td>1</td><td>47,094</td><td>63</td><td>53</td><td>PRJEB22338</td><td>LT960789</td></tr><tr><td rowspan="2">Lineage 3</td><td rowspan="2">CC3A</td><td>Complete</td><td>FLEC01</td><td>CNCM I-4395</td><td>Human feces, 2008</td><td>1</td><td>1,902,372</td><td>46</td><td>1,919</td><td>PRJEB22336</td><td>LT960777</td></tr><tr><td>Complete</td><td>J112 (112, JOUY-112)</td><td>CIP 110930</td><td>Dry sausage, 1990</td><td>1</td><td>31,701</td><td>55</td><td>36</td><td>PRJEB22336</td><td>LT960778</td></tr><tr><td rowspan="2">CC3B</td><td rowspan="2">CC3B</td><td>Complete</td><td>J54 (54, JOUY-54)</td><td>CNCM I-4393</td><td>Dry sausage, 1990</td><td>1</td><td>11,994</td><td>129</td><td>14</td><td>PRJEB22336</td><td>LT960779</td></tr><tr><td>Complete</td><td>T332 (332)<sup>c</sup></td><td>CIP 110934</td><td>Pork meat, 1987</td><td>1</td><td>10,871</td><td>452</td><td>9</td><td>PRJEB22336</td><td>LT960780</td></tr><tr><td rowspan="2">Admixed<sup>b</sup></td><td rowspan="2">Admixed<sup>b</sup></td><td>Draft</td><td>J18 (18, JOUY-18)</td><td>CIP 110934</td><td>Dry sausage, 1990</td><td>1</td><td>6,593</td><td>588</td><td>7</td><td>PRJEB22330</td><td>OBHN01000001 – OBHN01000038</td></tr><tr><td>Draft</td><td>J160x1 (160x1)</td><td>CIP 110932</td><td>Horse meat, 1981</td><td>1</td><td>1,842,916</td><td>61</td><td>1,857</td><td>PRJEB22333</td><td>OBHK01000033</td></tr><tr><td rowspan="2">Lineage 3</td><td rowspan="2">CC3A</td><td>Complete</td><td>FLEC01</td><td>CNCM I-4395</td><td>Human feces, 2008</td><td>1</td><td>51,764</td><td>504</td><td>62</td><td>PRJEB22336</td><td>OBHK01000034</td></tr><tr><td>Complete</td><td>J112 (112, JOUY-112)</td><td>CIP 110930</td><td>Dry sausage, 1990</td><td>1</td><td>31,701</td><td>55</td><td>36</td><td>PRJEB22336</td><td>LT960777</td></tr><tr><td rowspan="2">CC3A</td><td rowspan="2">CC3A</td><td>Complete</td><td>J112 (112, JOUY-112)</td><td>CNCM I-4393</td><td>Dry sausage, 1990</td><td>1</td><td>11,994</td><td>129</td><td>14</td><td>PRJEB22336</td><td>OBHN01000040</td></tr><tr><td>Complete</td><td>T332 (332)<sup>c</sup></td><td>CIP 110934</td><td>Pork meat, 1987</td><td>1</td><td>10,871</td><td>452</td><td>9</td><td>PRJEB22336</td><td>OBHN01000041</td></tr><tr><td rowspan="2">CC3B</td><td rowspan="2">CC3B</td><td>Complete</td><td>J54 (54, JOUY-54)</td><td>CNCM I-4393</td><td>Dry sausage, 1990</td><td>1</td><td>1,964,671</td><td>76</td><td>1,982</td><td>PRJEB22334</td><td>OBHN01000042</td></tr><tr><td>Complete</td><td>T332 (332)<sup>c</sup></td><td>CIP 110934</td><td>Pork meat, 1987</td><td>1</td><td>33,463</td><td>86</td><td>36</td><td>PRJEB22334</td><td>LT960791</td></tr><tr><td rowspan="2">Admixed<sup>b</sup></td><td rowspan="2">Admixed<sup>b</sup></td><td>Draft</td><td>J18 (18, JOUY-18)</td><td>CIP 110934</td><td>Dry sausage, 1990</td><td>1</td><td>13,205</td><td>241</td><td>15</td><td>PRJEB22356</td><td>LT960792</td></tr><tr><td>Draft</td><td>J160x1 (160x1)</td><td>CIP 110932</td><td>Horse meat, 1981</td><td>1</td><td>72,950</td><td>43</td><td>89</td><td>PRJEB22356</td><td>LT960787</td></tr><tr><td rowspan="2">Lineage 3</td><td rowspan="2">CC3A</td><td>Complete</td><td>FLEC01</td><td>CNCM I-4395</td><td>Human feces, 2008</td><td>1</td><td>1,902,372</td><td>46</td><td>1,919</td><td>PRJEB22336</td><td>LT960777</td></tr><tr><td>Complete</td><td>J112 (112, JOUY-112)</td><td>CIP 110930</td><td>Dry sausage, 1990</td><td>1</td><td>31,701</td><td>55</td><td>36</td><td>PRJEB22336</td><td>LT960778</td></tr><tr><td rowspan="2">CC3A</td><td rowspan="2">CC3A</td><td>Complete</td><td>J112 (112, JOUY-112)</td><td>CNCM I-4393</td><td>Dry sausage, 1990</td><td>1</td><td>11,994</td><td>129</td><td>14</td><td>PRJEB22336</td><td>OBHN01000040</td></tr><tr><td>Complete</td><td>T332 (332)<sup>c</sup></td><td>CIP 110934</td><td>Pork meat, 1987</td><td>1</td><td>10,871</td><td>452</td><td>9</td><td>PRJEB22336</td><td>OBHN01000041</td></tr><tr><td rowspan="2">CC3B</td><td rowspan="2">CC3B</td><td>Complete</td><td>J54 (54, JOUY-54)</td><td>CNCM I-4393</td><td>Dry sausage, 1990</td><td>1</td><td>1,964,671</td><td>76</td><td>1,982</td><td>PRJEB22334</td><td>OBHN01000042</td></tr><tr><td>Complete</td><td>T332 (332)<sup>c</sup></td><td>CIP 110934</td><td>Pork meat, 1987</td><td>1</td><td>33,463</td><td>86</td><td>36</td><td>PRJEB22356</td><td>LT960791</td></tr><tr><td rowspan="2">Admixed<sup>b</sup></td><td rowspan="2">Admixed<sup>b</sup></td><td>Draft</td><td>J18 (18, JOUY-18)</td><td>CIP 110934</td><td>Dry sausage, 1990</td><td>1</td><td>13,205</td><td>241</td><td>15</td><td>PRJEB22356</td><td>LT960792</td></tr><tr><td>Draft</td><td>J160x1 (160x1)</td><td>CIP 110932</td><td>Horse meat, 1981</td><td>1</td><td>72,950</td><td>43</td><td>89</td><td>PRJEB22330</td><td>OBHN01000001 – OBHN01000027</td></tr></tbody></table>

<footnote><sup>a</sup>According to Chailou et al. (2).</footnote>

<footnote><sup>b</sup>Multilocus sequence typing previously revealed that strain J18 is a mixture of the three lineages due to numerous recombination events (2).</footnote>

<footnote><sup>c</sup>CDS, coding sequence.</footnote>

<footnote><sup>d</sup>Plasmid pJ23A1 originated from the strain L. sakei 23, the chromosome of which has already been sequenced (3).</footnote>

<footnote><sup>e</sup>Plasmid p332A2 was sequenced from strain 332, the chromosome of which has been sequenced.</footnote>
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