# High-quality genome assembly of Listeria monocytogenes Lm208 (CNL895805): a domestic strain able to grow faster at low temperature when exogenous unsaturated fatty acids are present

Maud Darsonval, Hélène Gardon, Aurore Quilleré, Philippe Velge, Laurent Guillier, Florence Dubois-Brissonnet

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## To cite this version:

Maud Darsonval, Hélène Gardon, Aurore Quilleré, Philippe Velge, Laurent Guillier, et al.. High-quality genome assembly of Listeria monocytogenes Lm208 (CNL895805): a domestic strain able to grow faster at low temperature when exogenous unsaturated fatty acids are present. Microbiology Resource Announcements, 2025, 14 (8), pp.e0081624. 10.1128/mra.00816-24. hal-05162084

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Submitted on 29 Sep 2025

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# High-quality genome assembly of *Listeria monocytogenes* Lm208 (CNL895805): a domestic strain able to grow faster at low temperature when exogenous unsaturated fatty acids are present

Maud Darsonval,¹ Hélène Gardon,² Aurore Quilleré,¹ Philippe Velge,³ Laurent Guillier,⁴ Florence Dubois-Brissonnet¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 2.

**ABSTRACT** The genome of *Listeria monocytogenes* Lm208 strain has been sequenced and assembled. The draft genome has been automatically annotated. Considering its specific ability to grow faster at low temperatures in the presence of exogenous fatty acids, the annotation of genes related to fatty-acid metabolism was investigated using local and multiple sequence alignments.

**KEYWORDS** *Listeria monocytogenes*, fatty-acid metabolism, genome analysis

Listeria monocytogenes is a foodborne pathogen responsible for listeriosis. Lm208 (CNL895805, serotype 1/2a), isolated in 1992 from a sheep's brain, can grow faster at low temperature in the presence of exogenous unsaturated fatty acids (FA) (1, 2). Genomic DNA was extracted and purified from a 16-h culture in Tryptic Soy Broth (TSB) using the Wizard Genomic DNA Purification Kit (Promega, France). DNA sequencing was performed at the "Institut du Cerveau et de la Moëlle" (Paris, France). After quantification, DNA-seq libraries were prepared with the Nextera XT DNA Flex Library kit (Illumina, San Diego, USA). Whole Genome Sequencing (WGS) was performed on the NextSeq 500 system using a paired-end read length of 2 × 150 bp with the Illumina High Output kits. Raw reads (1,217,365 sequences; 151 bp) were analyzed using tools of the Galaxy portal (https://galaxy.migale.inrae.fr/). Trimming was performed with the following parameters: Initial IlluminaClip, Leading 3, Trailing 3, Sliding Window 4–20, and Minlen 125 bp (Trimmomatic v39.0) (3). The quality of 421,351 trimmed reads was checked with fastQC (v0.11.9) (4). De novo assembly was performed using SPAdes (v3.15.4) and followed by quality control (Quast v5.2.0) (5, 6). After ordering by progressiveMauve based on the genomic sequence of *L. monocytogenes* EGD-e (26 February 2015) (7), the size of the genome was 2,871,758 bp made of 12 contigs with a GC content of 37.9%, N50 value of 1,458,283 bp, L50 of 1, and an average coverage of 128×. Automatic annotation was performed with Prokka (v1.14.6) using the proteome of *L. monocytogenes* EGD-e as reference (UP000000817) (8).

2,824 predicted protein-coding genes were detected with 49 tRNAs and 4 rRNAs. 2,686 Coding Sequences (CDS) were assigned to a gene name based on the locus tag of *L. monocytogenes* EGD-e. Fifty CDS were identified using ListiWiki, ListeriOmics, or NBCI's database (9, 10). After enrichment, the remaining 120 CDS encoded hypothetical proteins. Lm208 does not harbour antibiotic resistance genes nor plasmids (Starnam v0.7.2.1) (11). Two phage regions were identified with PHASTEST (https://phastest.ca/): the *Listeria* phage A118 (NC_003216) prophage in the *comK* integration site and a partial *Streptococcus* phage T12 (NC_028700) interrupting the locus *lmo208_02875* (12–14). Contigs No. 3, 13, and 15 displayed repeated consensus regions of CRISPR and their

**Editor** Jason E. Stajich, University of California
Riverside, Riverside, California, USA

Address correspondence to
Florence Dubois-Brissonnet, florence.dubois-
brissonnet@agroparistech.fr.

The authors declare no conflict of interest.

**Received** 10 March 2025

**Accepted** 20 June 2025

**Published** 9 July 2025

Copyright © 2025 Darsonval et al. This is an
open-access article distributed under the terms of
the Creative Commons Attribution 4.0 International
license.
<table><caption>TABLE 1 Genome metrics of *L. monocytogenes* Lm208 and comparison to domestic reference strains EGD-e, EGD, ScottA, LO258, and 10403S</caption><thead><tr><th>Strain</th><th>Genomic element<sup>a</sup></th><th>RefSeq</th><th>ANI (%)</th><th>Contig no.</th><th>Length (Mb)</th><th>G + C content (%)</th><th>No. of CDS</th><th>No. of tRNA</th><th>No. of rRNAs</th><th>Source</th><th>CC</th></tr></thead><tbody><tr><td>Lm208</td><td>Chr</td><td>GCF_048381475.1</td><td>100</td><td>12</td><td>2.87</td><td>37.9</td><td>2,824</td><td>49</td><td>4</td><td>Sheep's brain</td><td>7</td></tr><tr><td>EGD-e</td><td>Chr</td><td>GCF_000196035.1</td><td>98.94</td><td>1</td><td>2.94</td><td>38.0</td><td>2,867</td><td>67</td><td>18</td><td>Derivative of EGD</td><td>9</td></tr><tr><td>EGD</td><td>Chr</td><td>GCF_000582845.1</td><td>99.93</td><td>1</td><td>2.91</td><td>38.0</td><td>2,818</td><td>67</td><td>18</td><td>Guinea pig tissue</td><td>7</td></tr><tr><td>10403S</td><td>Chr</td><td>GCF_000168695.2</td><td>99.99</td><td>1</td><td>2.90</td><td>38.0</td><td>2,802</td><td>67</td><td>6</td><td>Human skin lesions</td><td>7</td></tr><tr><td>ScottA</td><td>Chr</td><td>GCF_000212455.1</td><td>94.94</td><td>5</td><td>3.03</td><td>38</td><td>2,934</td><td>67</td><td>6</td><td>Listeriosis outbreak</td><td>7</td></tr><tr><td>LO28</td><td>Chr</td><td>GCF_021378215.1</td><td>98.90</td><td>1</td><td>2.98</td><td>38</td><td>2,911</td><td>67</td><td>6</td><td>Pregnant carrier</td><td>9</td></tr></tbody></table>

associated caspase proteins (CRISPRCasFinder; https://crisprcas.i2bc.paris-saclay.fr/) (15). Clonal complex (CC) and lineage were defined *in silico* using the BIGSdb database (http://bigsdb.pasteur.fr/listeria), which revealed that Lm208 belongs to lineage II and CC7, clones rarely related to food isolates (16). Lm208 highlights high similarity with the four reference strains with a maximum of average nucleotide identity (ANI) at 99.99% with *L. monocytogenes* 10403S and a minimum of ANI at 94.94% with *L. monocytogenes* ScottA (FastANI (v1.3) (Table 1; 17, 18)).

After automatic annotation, the annotation of Fak and Fab proteins, related to FA metabolism, was deeply investigated based on literature and local or multiple sequence alignments (1). One FakA and two FakB proteins were identified by BLASTp using the well-described *Staphylococcus aureus* FakAB system (Q2FHL2.1; ABD20605.1; ABD22554.1) as query sequences (18, 19). Eleven Fab proteins were found by Prokka or by NCBI's BLASTp database and multiple sequence alignment (ClustalOmega v1.2.4) with 114 Fab sequences from *Streptococcaceae* and *Bacillaceae* (20). Phenotypic investigation is needed to identify the genetic marker related to its specific ability to grow faster in the presence of unsaturated FA.

## ACKNOWLEDGMENTS

This work benefited from equipment and services from the iGenSeq core facility (Genotyping and sequencing), at ICM.

## AUTHOR AFFILIATIONS

## AUTHOR ORCIDs

Maud Darsonval http://orcid.org/0000-0003-1762-3303

Hélène Gardon http://orcid.org/0000-0001-8976-1372

Aurore Quilleré http://orcid.org/0000-0002-2720-8878

Philippe Velge http://orcid.org/0000-0002-8201-0194

Laurent Guillier http://orcid.org/0000-0002-7867-2937

Florence Dubois-Brissonnet http://orcid.org/0000-0003-2998-7518

## AUTHOR CONTRIBUTIONS

Maud Darsonval, Conceptualization, Data curation, Formal analysis, Investigation, Supervision, Writing – original draft, Writing – review and editing | Hélène Gardon, Data curation, Investigation | Philippe Velge, Resources | Laurent Guillier, Data curation, Methodology, Writing – review and editing | Florence Dubois-Brissonnet, Conceptualization, Supervision, Writing – review and editing.

<footnote><sup>a</sup>Chr: chromosome.</footnote>

<footnote n="1">¹Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, Jouy-en-Josas, France</footnote>

<footnote n="2">²Université Paris-Saclay, INRAE, AgroParisTech, UMR SAYFOOD, Palaiseau, France</footnote>

<footnote n="3">³INRAE, Université de Tours, ISP, Nouzilly, France</footnote>

<footnote n="4">⁴Direction de l'évaluation des risques, Agence nationale de sécurité sanitaire de l'alimentation de l'environnement et du travail (ANSES), Maisons-Alfort, France</footnote>
DATA AVAILABILITY

This whole-genome shotgun project has been deposited at GenBank under the accession number (JBLUWX000000000) and in the NCBI Sequence Read Archive (SRA SRR29855365) under BioProject accession number PRJNA1074122 and BioSample number SAMN39851069, respectively. The version described in this paper is the first version (JBLUWX000000000.1).

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