# Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing

Emmanuel Szadkowski, Jacques Lagnel, Nasradin Touhami, Amalia Sayeh, Céline Lopez-Roques, Olivier Bouchez, Véronique Lefebvre

► To cite this version:

Emmanuel Szadkowski, Jacques Lagnel, Nasradin Touhami, Amalia Sayeh, Céline Lopez-Roques, et al.. Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing. Microbiology Resource Announcements, 2023, 12 (12), 10.1128/mra.00196-23. [https://doi.org/10.1128/mra.00196-23](https://doi.org/10.1128/mra.00196-23)

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# Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing

Emmanuel Szadkowski, Jacques Lagnel, Nasradin Touhami, Amalia Sayeh, Céline Lopez-Roques, Olivier Bouchez, Véronique Lefebvre

► To cite this version:

Emmanuel Szadkowski, Jacques Lagnel, Nasradin Touhami, Amalia Sayeh, Céline Lopez-Roques, et al.. Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing. Microbiology Resource Announcements, 2023, 12 (12), 10.1128/mra.00196-23. [https://doi.org/10.1128/mra.00196-23](https://doi.org/10.1128/mra.00196-23)

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Submitted on 26 Mar 2024

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entific research documents, whether they are pub-
lished or not. The documents may come from
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abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# *Phytophthora capsici* genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing

Emmanuel Szadkowski,¹ Jacques Lagnel,¹ Nasradin Touhami,¹ Amalia Sayeh,² Céline Lopez-Roques,² Olivier Bouchez,² Véronique Lefebvre¹

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

**ABSTRACT** The oomycete *Phytophthora capsici* is a common pathogen of the Solanaceae and Cucurbitaceae families. An improved assembly for the reference isolate LT1534 was constructed using Oxford Nanopore Technologies and Illumina data. Additionally, an unpolished assembly was produced for the European isolate Pc285 collected on chili pepper using Oxford Nanopore reads.

**KEYWORDS** plant pathogens, oomycetes

Phytophthora capsici is a widespread pathogen that causes damages to many plant species, and particularly the species of the Solanaceae and Cucurbitaceae families. Several improved genomes using long-read technologies have recently been published for the cucurbit-infecting strain LT1534 (1), its original backcrossing recurrent parent LT263 (2), and several other chili pepper-infecting strains collected in China (3) and Korea (4). Here, we have produced long-read nanopore assemblies of the reference isolate LT1534 and provided an unpolished assembly of the isolate Pc285 that was sampled from chili pepper in France.

The two *P. capsici* isolates LT1534 (Pc331 in the INRAE GAFL collection) and Pc285 were grown on a clarified liquid V8 medium, supplemented with a cocktail of antibiotics, for 7 days in the dark, and DNA extraction was performed following the protocol of Panabières and Le Berre (5).

Library preparation and sequencing were performed at the INRAE GeT-PlaGe core facility, according to the manufacturer's instructions, "1D gDNA selecting for long reads (SQK-LSK109)." At each step, DNA was quantified using the Qubit dsDNA HS Assay Kit (Life Technologies). DNA purity was tested using the NanoDrop (Thermo Fisher) and size distribution, and degradation was assessed using the Agilent Fragment Analyzer DNF-464 HS Large Fragment Kit. Purification steps were performed using AMPure XP beads (Beckman Coulter). For LT1534, 9 µg of DNA was purified, and a size selection step using a Short-Read Eliminator XS Kit (Circulomics) was performed. For Pc285, 5 µg of DNA was purified and then sheared at 35 kb using the Megaruptor system (Diagenode). For both prepared samples, a one-step DNA damage repair + END-repair + dA tail of double-stranded DNA fragments was performed on 2 µg of sample. Then, adapters were ligated to the libraries. Each library was loaded onto one R9.4.1 flow cell and sequenced on a GridION instrument (Gridion-release 18.12.4–1 and 19.06.9–1) at 27 fmol and 21 fmol, respectively, within 48 h. The base calling was performed by Guppy 2.0.10–1 and 3.0.6–1.

Sequencing produced 21.1 Gbp for LT1534 with 1.4 million reads and a median read length of 13.0 kbp. Around 17.5 Gbp was obtained for Pc285, representing 1.3 million reads with a median read length of 11.3 kbp. Nanopore reads were preprocessed with Porechop (https://github.com/rrwick/Porechop, version 0.2.4), followed for Pc285 by Filtlong read selection (QC >7, read length >3 kbp, https://github.com/rrwick/Filtlong,

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

Address correspondence to Emmanuel Szadkowski,
emmanuel.szadkowski@inrae.fr, or Véronique
Lefebvre, veronique.lefebvre@inrae.fr.

The authors declare no conflict of interest.

See the funding table on p. 3.

Received 5 April 2023

Accepted 10 October 2023

Published 10 November 2023

Copyright © 2023 Szadkowski et al. This is an
open-access article distributed under the terms of
the Creative Commons Attribution 4.0 International
license.
<figure><img src="image_2.png" /></figure>

# *Phytophthora capsici* genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing

Emmanuel Szadkowski,¹ Jacques Lagnel,¹ Nasradin Touhami,¹ Amalia Sayeh,² Céline Lopez-Roques,² Olivier Bouchez,² Véronique Lefebvre¹

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

**ABSTRACT** The oomycete *Phytophthora capsici* is a common pathogen of the Solanaceae and Cucurbitaceae families. An improved assembly for the reference isolate LT1534 was constructed using Oxford Nanopore Technologies and Illumina data. Additionally, an unpolished assembly was produced for the European isolate Pc285 collected on chili pepper using Oxford Nanopore reads.

**KEYWORDS** plant pathogens, oomycetes

Phytophthora capsici is a widespread pathogen that causes damages to many plant species, and particularly the species of the Solanaceae and Cucurbitaceae families. Several improved genomes using long-read technologies have recently been published for the cucurbit-infecting strain LT1534 (1), its original backcrossing recurrent parent LT263 (2), and several other chili pepper-infecting strains collected in China (3) and Korea (4). Here, we have produced long-read nanopore assemblies of the reference isolate LT1534 and provided an unpolished assembly of the isolate Pc285 that was sampled from chili pepper in France.

The two *P. capsici* isolates LT1534 (Pc331 in the INRAE GAFL collection) and Pc285 were grown on a clarified liquid V8 medium, supplemented with a cocktail of antibiotics, for 7 days in the dark, and DNA extraction was performed following the protocol of Panabières and Le Berre (5).

Library preparation and sequencing were performed at the INRAE GeT-PlaGe core facility, according to the manufacturer's instructions, "1D gDNA selecting for long reads (SQK-LSK109)." At each step, DNA was quantified using the Qubit dsDNA HS Assay Kit (Life Technologies). DNA purity was tested using the NanoDrop (Thermo Fisher) and size distribution, and degradation was assessed using the Agilent Fragment Analyzer DNF-464 HS Large Fragment Kit. Purification steps were performed using AMPure XP beads (Beckman Coulter). For LT1534, 9 µg of DNA was purified, and a size selection step using a Short-Read Eliminator XS Kit (Circulomics) was performed. For Pc285, 5 µg of DNA was purified and then sheared at 35 kb using the Megaruptor system (Diagenode). For both prepared samples, a one-step DNA damage repair + END-repair + dA tail of double-stranded DNA fragments was performed on 2 µg of sample. Then, adapters were ligated to the libraries. Each library was loaded onto one R9.4.1 flow cell and sequenced on a GridION instrument (Gridion-release 18.12.4–1 and 19.06.9–1) at 27 fmol and 21 fmol, respectively, within 48 h. The base calling was performed by Guppy 2.0.10–1 and 3.0.6–1.

Sequencing produced 21.1 Gbp for LT1534 with 1.4 million reads and a median read length of 13.0 kbp. Around 17.5 Gbp was obtained for Pc285, representing 1.3 million reads with a median read length of 11.3 kbp. Nanopore reads were preprocessed with Porechop (https://github.com/rrwick/Porechop, version 0.2.4), followed for Pc285 by Filtlong read selection (QC >7, read length >3 kbp, https://github.com/rrwick/Filtlong,

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

Address correspondence to Emmanuel Szadkowski,
emmanuel.szadkowski@inrae.fr, or Véronique
Lefebvre, veronique.lefebvre@inrae.fr.

The authors declare no conflict of interest.

See the funding table on p. 3.

Received 5 April 2023

Accepted 10 October 2023

Published 10 November 2023

Copyright © 2023 Szadkowski 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 Overview of the recent *Phytophthora capsici* genome assembly metrics</caption><thead><tr><th>Article</th><th>Lee et al. (4)</th><th>Shi et al. (3)</th><th>Stajich et al. (1)</th><th>This article</th></tr></thead><tbody><tr><td>Isolate</td><td>JHAI1-7</td><td>KPC-7</td><td>MY-1</td><td>SD33</td><td>LT1534</td><td>LT1534</td><td>Pc285</td></tr><tr><td>Assembly statistics</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Total number of contigs</td><td>472</td><td>548</td><td>521</td><td>194</td><td>782</td><td>203</td><td>213</td></tr><tr><td>Total length (bp)</td><td>76,839,304</td><td>74,832,015</td><td>76,624,583</td><td>100,526,817</td><td>94,176,027</td><td>92,550,228</td><td>75,652,381</td></tr><tr><td>Average length (bp)</td><td>162,795</td><td>136,555</td><td>147,072</td><td>518,179</td><td>120,430</td><td>455,912</td><td>355,176</td></tr><tr><td>Median length (bp)</td><td>29,583</td><td>26,079</td><td>26,730</td><td>296,807</td><td>26,215</td><td>347,626</td><td>209,050</td></tr><tr><td>Min length (bp)</td><td>1,229</td><td>657</td><td>723</td><td>11,508</td><td>2,527</td><td>16,903</td><td>39,489</td></tr><tr><td>Max length (bp)</td><td>2,514,355</td><td>2,715,842</td><td>2,720,928</td><td>4,147,862</td><td>4,616,793</td><td>2,689,262</td><td>2,757,130</td></tr><tr><td>Total Ns</td><td>1,067</td><td>1,304</td><td>1,409</td><td>0</td><td>100</td><td>0</td><td>0</td></tr><tr><td>Total %GC</td><td>51.01</td><td>50.96</td><td>50.96</td><td>50.82</td><td>51.19</td><td>50.94</td><td>50.8</td></tr><tr><td>N50 length (bp)</td><td>798,104</td><td>663,153</td><td>635,553</td><td>1,013,378</td><td>485,876</td><td>714,920</td><td>609,692</td></tr><tr><td>Busco protist_ensembl (n = 215)</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Complete</td><td>99.5%</td><td>99.0%</td><td>100.0%</td><td>95.4%</td><td>99.0%</td><td>97.2%</td><td>78.6%</td></tr><tr><td>Single</td><td>95.3%</td><td>98.1%</td><td>98.6%</td><td>72.1%</td><td>82.3%</td><td>76.2%</td><td>67.9%</td></tr><tr><td>Duplicated</td><td>4.2%</td><td>0.9%</td><td>1.4%</td><td>23.3%</td><td>16.7%</td><td>20.5%</td><td>10.7%</td></tr><tr><td>False</td><td>0.0%</td><td>0.0%</td><td>0.0%</td><td>0.5%</td><td>0.0%</td><td>0.0%</td><td>2.8%</td></tr><tr><td>Missing</td><td>0.5%</td><td>1.0%</td><td>0.0%</td><td>4.1%</td><td>1.0%</td><td>2.8%</td><td>18.6%</td></tr></tbody></table>

version 0.2.0). Canu version 1.8 (6) correction was applied, and assembly was performed using SMARTdenovo version 1.11 (7). Contigs of LT1534 were further polished in two passes with Pilon version 1.23 (8) using LT1534 Illumina single-ended reads published by Lamour et al. (9). The total length of the assembly was smaller for Pc285 (75.7 Mbp with 209.0 kbp contig median length) than for LT1534 (92.6 Mbp with 347.6 kbp contig median length), with values comparable to other genome assemblies (Table 1). The assembly resulted in an N50 length of 715 kbp and 610 kbp, and 50% of the assembly is contained in 41 and 39 contigs for LT1534 and Pc285, respectively.

Busco (version 3.0.2) score was assessed for the LT1534 assembly on the "protist_ensembl" data set, achieving 97.2% completeness out of 215 genes (76.2% unique, 20.5% duplicated, 0% fragmented, and 2.8% missing) in the same range of other papers (Table 1). Given the unpolished nature of the Pc285 assembly, its Busco score is lower with 78.6% of completeness (Table 1).

LT1534 annotation was performed using Funannotate 1.8.14 with default parameters (10). Briefly, gene prediction of repeat-masked contigs (using tantan) was performed using RefSeq proteins from the NCBI database (filtered on txid4783) and without RNA-Seq experimental data, producing 23,347 predicted genes including 2,100 genes coding tRNAs. Functional annotation was completed using InterProScan (version 5.42–78.0).

## ACKNOWLEDGMENTS

We acknowledge Professor Kurt Lamour, who kindly supplied a mycelium sample of the LT1534 isolate. INRAE Plant Biology and Breeding Division funded the data production under the PhytAg project. We are grateful to the INRAE GenoToul bioinformatics facility (https://doi.org/10.15454/1.5572369328961167E12) for providing computing and storage resources. Analyses were performed on the INRAE GenoToul computing farm (Toulouse, France).

## AUTHOR AFFILIATIONS

<footnote n="1">¹INRAE, GAFL, Montfavet, France</footnote>

<footnote n="2">²INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France</footnote>
<table><caption>TABLE 1 Overview of the recent *Phytophthora capsici* genome assembly metrics</caption><thead><tr><th>Article</th><th>Lee et al. (4)</th><th>Shi et al. (3)</th><th>Stajich et al. (1)</th><th>This article</th></tr></thead><tbody><tr><td>Isolate</td><td>JHAI1-7</td><td>KPC-7</td><td>MY-1</td><td>SD33</td><td>LT1534</td><td>LT1534</td><td>Pc285</td></tr><tr><td>Assembly statistics</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Total number of contigs</td><td>472</td><td>548</td><td>521</td><td>194</td><td>782</td><td>203</td><td>213</td></tr><tr><td>Total length (bp)</td><td>76,839,304</td><td>74,832,015</td><td>76,624,583</td><td>100,526,817</td><td>94,176,027</td><td>92,550,228</td><td>75,652,381</td></tr><tr><td>Average length (bp)</td><td>162,795</td><td>136,555</td><td>147,072</td><td>518,179</td><td>120,430</td><td>455,912</td><td>355,176</td></tr><tr><td>Median length (bp)</td><td>29,583</td><td>26,079</td><td>26,730</td><td>296,807</td><td>26,215</td><td>347,626</td><td>209,050</td></tr><tr><td>Min length (bp)</td><td>1,229</td><td>657</td><td>723</td><td>11,508</td><td>2,527</td><td>16,903</td><td>39,489</td></tr><tr><td>Max length (bp)</td><td>2,514,355</td><td>2,715,842</td><td>2,720,928</td><td>4,147,862</td><td>4,616,793</td><td>2,689,262</td><td>2,757,130</td></tr><tr><td>Total Ns</td><td>1,067</td><td>1,304</td><td>1,409</td><td>0</td><td>100</td><td>0</td><td>0</td></tr><tr><td>Total %GC</td><td>51.01</td><td>50.96</td><td>50.96</td><td>50.82</td><td>51.19</td><td>50.94</td><td>50.8</td></tr><tr><td>N50 length (bp)</td><td>798,104</td><td>663,153</td><td>635,553</td><td>1,013,378</td><td>485,876</td><td>714,920</td><td>609,692</td></tr><tr><td>Busco protist_ensembl (n = 215)</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Complete</td><td>99.5%</td><td>99.0%</td><td>100.0%</td><td>95.4%</td><td>99.0%</td><td>97.2%</td><td>78.6%</td></tr><tr><td>Single</td><td>95.3%</td><td>98.1%</td><td>98.6%</td><td>72.1%</td><td>82.3%</td><td>76.2%</td><td>67.9%</td></tr><tr><td>Duplicated</td><td>4.2%</td><td>0.9%</td><td>1.4%</td><td>23.3%</td><td>16.7%</td><td>20.5%</td><td>10.7%</td></tr><tr><td>False</td><td>0.0%</td><td>0.0%</td><td>0.0%</td><td>0.5%</td><td>0.0%</td><td>0.0%</td><td>2.8%</td></tr><tr><td>Missing</td><td>0.5%</td><td>1.0%</td><td>0.0%</td><td>4.1%</td><td>1.0%</td><td>2.8%</td><td>18.6%</td></tr></tbody></table>

version 0.2.0). Canu version 1.8 (6) correction was applied, and assembly was performed using SMARTdenovo version 1.11 (7). Contigs of LT1534 were further polished in two passes with Pilon version 1.23 (8) using LT1534 Illumina single-ended reads published by Lamour et al. (9). The total length of the assembly was smaller for Pc285 (75.7 Mbp with 209.0 kbp contig median length) than for LT1534 (92.6 Mbp with 347.6 kbp contig median length), with values comparable to other genome assemblies (Table 1). The assembly resulted in an N50 length of 715 kbp and 610 kbp, and 50% of the assembly is contained in 41 and 39 contigs for LT1534 and Pc285, respectively.

Busco (version 3.0.2) score was assessed for the LT1534 assembly on the "protist_ensembl" data set, achieving 97.2% completeness out of 215 genes (76.2% unique, 20.5% duplicated, 0% fragmented, and 2.8% missing) in the same range of other papers (Table 1). Given the unpolished nature of the Pc285 assembly, its Busco score is lower with 78.6% of completeness (Table 1).

LT1534 annotation was performed using Funannotate 1.8.14 with default parameters (10). Briefly, gene prediction of repeat-masked contigs (using tantan) was performed using RefSeq proteins from the NCBI database (filtered on txid4783) and without RNA-Seq experimental data, producing 23,347 predicted genes including 2,100 genes coding tRNAs. Functional annotation was completed using InterProScan (version 5.42–78.0).

## ACKNOWLEDGMENTS

We acknowledge Professor Kurt Lamour, who kindly supplied a mycelium sample of the LT1534 isolate. INRAE Plant Biology and Breeding Division funded the data production under the PhytAg project. We are grateful to the INRAE GenoToul bioinformatics facility (https://doi.org/10.15454/1.5572369328961167E12) for providing computing and storage resources. Analyses were performed on the INRAE GenoToul computing farm (Toulouse, France).

## AUTHOR AFFILIATIONS

<footnote n="1">¹INRAE, GAFL, Montfavet, France</footnote>

<footnote n="2">²INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France</footnote>
## AUTHOR ORCIDs

Emmanuel Szadkowski http://orcid.org/0000-0003-0318-8953

Jacques Lagnel http://orcid.org/0000-0002-2967-1639

Céline Lopez-Roques http://orcid.org/0000-0003-2529-7958

Olivier Bouchez http://orcid.org/0000-0002-7255-0058

Véronique Lefebvre http://orcid.org/0000-0001-9916-8433

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s) Author(s)</td></tr></thead><tbody><tr><td>Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)</td><td>Emmanuel Szadkowski</td></tr></tbody></table>

## AUTHOR CONTRIBUTIONS

Emmanuel Szadkowski, Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Validation, Writing – original draft, Writing – review and editing | Jacques Lagnel, Conceptualization, Methodology, Software, Validation, Writing – review and editing | Nasradin Touhami, Investigation, Methodology, Resources, Writing – review and editing | Amalia Sayeh, Data curation, Investigation, Resources, Writing – review and editing | Céline Lopez-Roques, Data curation, Methodology, Validation, Writing – review and editing | Olivier Bouchez, Conceptualization, Data curation, Methodology, Supervision, Writing – review and editing | Véronique Lefebvre, Writing – review and editing

## DATA AVAILABILITY

Raw data, assemblies, and annotations for isolates LT1534 and Pc285 are available in Project PRJEB60432 of the ENA repository.

## REFERENCES

1. Stajich JE, Vu AL, Judelson HS, Vogel GM, Gore MA, Carlson MO, Devitt N, Jacobi J, Mudge J, Lamour KH, Smart CD. 2021. High-quality reference genome sequence for the oomycete vegetable pathogen *Phytophthora capsici* strain Lt1534. Microbiol Resour Announc 10:e0029521. https://doi.org/10.1128/MRA.0029521-21

2. Cui C, Herlihy JH, Bombarely A, McDowell JM, Haak DC. 2019. Draft assembly of *Phytophthora capsici* from long-read sequencing uncovers complexity. MPMI 32:1559–1563. https://doi.org/10.1094/MPMI-04-19-0103-TA

3. Shi J, Ye W, Ma D, Yin J, Zhang Z, Wang Y, Qiao Y. 2021. Improved whole-genome sequence of *Phytophthora capsici* generated by long-read sequencing. Mol Plant Microbe Interact 34:866–869. https://doi.org/10.1094/MPMI-12-20-0356-A

4. Lee JH, Siddique MI, Kwon JK, Kang BC. 2021. Comparative genomic analysis reveals genetic variation and adaptive evolution in the pathogenicity-related genes of *Phytophthora capsici*. Front Microbiol 12:694136. https://doi.org/10.3389/fmicb.2021.694136

5. Panabières F, Le Berre JY. 1999. A family of repeated DNA in the genome of the oomycete plant pathogen *Phytophthora cryptogea*. Curr Genet 36:105–112. https://doi.org/10.1007/s002940050479

6. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. https://doi.org/10.1101/gr.215087.116

7. Liu H, Wu S, Li A, Ruan J. 2021. SMARTdenovo: a de novo assembler using long noisy reads. Gigabyte 2021:1–9. https://doi.org/10.46471/gigabyte.15

8. 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

9. Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, et al. 2012. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen *Phytophthora capsici*. Mol Plant Microbe Interact 25:1350–1360. https://doi.org/10.1094/MPMI-02-12-0028-R

10. Palmer JM, Stajich JE. 2020. Funannotate v1.8.1: eukaryotic genome annotation. https://doi.org/10.5281/zenodo.1134477
## AUTHOR ORCIDs

Emmanuel Szadkowski http://orcid.org/0000-0003-0318-8953

Jacques Lagnel http://orcid.org/0000-0002-2967-1639

Céline Lopez-Roques http://orcid.org/0000-0003-2529-7958

Olivier Bouchez http://orcid.org/0000-0002-7255-0058

Véronique Lefebvre http://orcid.org/0000-0001-9916-8433

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s) Author(s)</td></tr></thead><tbody><tr><td>Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)</td><td>Emmanuel Szadkowski</td></tr></tbody></table>

## AUTHOR CONTRIBUTIONS

Emmanuel Szadkowski, Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Validation, Writing – original draft, Writing – review and editing | Jacques Lagnel, Conceptualization, Methodology, Software, Validation, Writing – review and editing | Nasradin Touhami, Investigation, Methodology, Resources, Writing – review and editing | Amalia Sayeh, Data curation, Investigation, Resources, Writing – review and editing | Céline Lopez-Roques, Data curation, Methodology, Validation, Writing – review and editing | Olivier Bouchez, Conceptualization, Data curation, Methodology, Supervision, Writing – review and editing | Véronique Lefebvre, Writing – review and editing

## DATA AVAILABILITY

Raw data, assemblies, and annotations for isolates LT1534 and Pc285 are available in Project PRJEB60432 of the ENA repository.

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