# Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties

Liya Zhu, Céline Lopez-Roques, Marine Sallaberry, Kory Jason, Laurent

Ouerdane, Sylvie Mazurier, Philippe Lemanceau, Barbara Pivato

► To cite this version:

Liya Zhu, Céline Lopez-Roques, Marine Sallaberry, Kory Jason, Laurent Ouerdane, et al. Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties. Microbiology Resource Announcements, 2025, 14 (8), 10.1128/mra.00570-25. hal-05223853

HAL Id: hal-05223853

https://univ-pau.hal.science/hal-05223853v1

Submitted on 26 Aug 2025

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Distributed under a Creative Commons Attribution 4.0 International License
# Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties

Liya Zhu,¹ Céline Lopez-Roques,² Marine Sallaberry,² Kory Jason,² Laurent Ouerdane,³ Sylvie Mazurier,¹ Philippe Lemanceau,¹ Barbara Pivato¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 5.

**ABSTRACT** Here, we report the whole-genome sequencing of 38 siderophore-producing bacterial strains isolated from the root systems of two pea and one wheat varieties. High-quality genomic data for each isolate was generated using PacBio HiFi sequencing, producing 6.1 Gb of HiFi reads and achieving an average assembly completeness of 98.85%.

**KEYWORDS** bacterial isolates, root system, iron, siderophore

Iron is abundant in soils but mostly unavailable to plants and microorganisms (1). Many bacteria secrete siderophores—iron-chelating secondary metabolites—that facilitate iron acquisition and enhance plant uptake (2–4). Beyond nutrition, siderophores mediate microbial communities' interactions, including cooperation, competition, and exploitation, influencing community assembly, stability, and plant health (5, 6).

Here, we report whole-genome sequencing of 38 siderophore-producing bacterial strains isolated from the root system of two pea (*Pisum sativum* L., Balltrap and Dexter) and one wheat (*Triticum aestivum* L., Flamenko) varieties (7). Plants were grown in two previously characterized soil types (7) under laboratory conditions (47°19′1.268″ N, 5°4′16.075″ E). Roots were rinsed, crushed, and serial dilutions plated on 0.1× Tryptic Soy Agar (TSA, Condalab) supplemented with 200 µg mL⁻¹ cycloheximide (Sigma). Plates were incubated at 25°C for 5 days. Colonies were purified by single-colony isolation and screened for siderophore production using CAS medium (8, 9). Positive isolates were coded (Table 1) and stored at −80°C in 0.1× Tryptic Soy Broth (TSB, Condalab) with 12.5% glycerol (Promega), after 3–5 days of liquid growth.

For DNA extraction, strains were recultivated in 0.1 × TSB and harvested at the end of exponential phase. Genomic DNA was extracted using Genomic-tip 20 /G Kit (Qiagen), quantified with Qubit dsDNA HS (ThermoFisher), and quality-checked by Nanodrop (ThermoFisher) and Agilent Fragment Analyzer (DNA 50 kb kit) (TECAN Infinite 200 Pro). Two µg of DNA per sample were purified and sheared to ~10 kb, using either FastPrep96 (MP Biomedicals) or Megaruptor 3 (Diagenode); no size selection followed shearing.

Libraries were prepared from 500 ng sheared DNA using the SMRTbell Express Template Prep Kit 2.0 (PacBio), ligated with barcoded blunt-end hairpin adapters, treated with exonucleases, and pooled equimolarly.

Sequencing was performed on the PacBio Sequel II system using the Binding Kit 3.2 and Sequencing Kit 2.0, with 100 pM loading concentration, two-hours pre-extension, and 30 hours movie per SMRT cell (3 cells total), using Sequel II DNA Polymerase 2.2.

Subreads were processed using SMRT Link to generate Circular Consensus Sequences (CCS, or HiFi reads), with automatic adapter removal and Q ≥ 20 filtering, generating 6.1 Gb of HiFi reads. Read counts and N50 values are in Table 1.

HiFi reads were assembled with Flye v. 2.9.5 (10). Assembly quality was assessed with BUSCO v5.7.1 (11) with alphaproteobacteria_odb10 data set (11) and QUAST v5.2.0 (12),

Editor David A. Baltrus, The University of Arizona,
Tucson, Arizona, USA

Address correspondence to Barbara Pivato,
barbara.pivato@inrae.fr.

The authors declare no conflict of interest.

See the funding table on p. 5.

Received 4 June 2025

Accepted 14 July 2025

Published 23 July 2025

Copyright © 2025 Zhu 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 Taxonomic identification, related metadata, HiFi reads statistics, genome assembly statistics (BUSCO with the alphaproteobacteria_odb10 data set and QUAST), and accession numbers for the 38 bacterial whole-genome sequences<sup>a</sup></caption><thead><tr><th rowspan="2">Strain Code<sup>b</sup></th><th rowspan="2">Taxonomic Affiliation</th><th colspan="2">Metadata</th><th colspan="2">HiFi reads statistics</th><th colspan="6">Genome assembly statistics</th><th colspan="6">Accession numbers</th></tr><tr><th>Plant</th><th>Soil type</th><th>Read counts</th><th>N50 (bp)</th><th>BUSCO Results</th><th># Contigs</th><th>Total Length (bp)</th><th>N50 (bp)</th><th>L50</th><th>GC (%)</th><th>Coverage (x)</th><th>Biosample accession No.</th><th>SRA accession No.</th><th>Assembly accession No.</th></tr></thead><tbody><tr><td>36a20</td><td>Acidovorax facilis</td><td>Wheat</td><td>Auzeville</td><td>21,525</td><td>14,783</td><td>C:99.2%<br/>[S:98.4%,D:0.8%]F:0.8%,M:0.0%,n:124</td><td>3</td><td>5,809,211</td><td>5493086</td><td>1</td><td>64.34</td><td>40</td><td>SAMN47300670</td><td>SRX27953989</td><td>GCA_050627005.1</td></tr><tr><td>37c5</td><td>Acidovorax facilis</td><td>Wheat</td><td>Auzeville</td><td>42,293</td><td>11,357</td><td>C:99.2%<br/>[S:98.4%,D:0.8%]F:0.8%,M:0.0%,n:124</td><td>3</td><td>5,806,590</td><td>5490465</td><td>1</td><td>64.34</td><td>61</td><td>SAMN47300673</td><td>SRX27954012</td><td>GCA_050626955.1</td></tr><tr><td>21a14</td><td>Arthrobacter sp. 21a14</td><td>Pea Dexter</td><td>Auzeville</td><td>25,977</td><td>10,022</td><td>C:99.2%<br/>[S:98.4%,D:0.8%]F:0.8%,M:0.0%,n:124</td><td>2</td><td>5,652,313</td><td>5437079</td><td>1</td><td>61.55</td><td>35</td><td>SAMN47300684</td><td>SRX27953995</td><td>GCA_050627125.1</td></tr><tr><td>20a6</td><td>Arthrobacter sp. 20a6</td><td>Pea Dexter</td><td>Epoisses</td><td>16,628</td><td>10,117</td><td>C:99.2%<br/>[S:98.4%,D:0.8%]F:0.8%,M:0.0%,n:124</td><td>3</td><td>5,655,880</td><td>5437081</td><td>1</td><td>61.55</td><td>22</td><td>SAMN47300702</td><td>SRX27954015</td><td>GCA_050710035.1</td></tr><tr><td>25a33</td><td>Enterobacter kobei</td><td>Pea Dexter</td><td>Auzeville</td><td>37,318</td><td>16,388</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4,762,226</td><td>4623341</td><td>1</td><td>55.01</td><td>94</td><td>SAMN47300682</td><td>SRX27953993</td><td>GCA_050627095.1</td></tr><tr><td>25b15</td><td>Enterobacter kobei</td><td>Pea Dexter</td><td>Auzeville</td><td>17,868</td><td>16,800</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4,762,226</td><td>4623341</td><td>1</td><td>55.01</td><td>46</td><td>SAMN47300685</td><td>SRX27953996</td><td>GCA_050627105.1</td></tr><tr><td>4a1</td><td>Enterobacter kobei</td><td>Pea Balltrap</td><td>Epoisses</td><td>15,809</td><td>15,755</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4,762,221</td><td>4623341</td><td>1</td><td>55.01</td><td>40</td><td>SAMN47300696</td><td>SRX27954008</td><td>GCA_050626945.1</td></tr><tr><td>9c6</td><td>Enterobacter kobei</td><td>Pea Balltrap</td><td>Auzeville</td><td>27,194</td><td>16,335</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4,762,226</td><td>4623341</td><td>1</td><td>55.01</td><td>71</td><td>SAMN47300678</td><td>SRX27954025</td><td>GCA_050626885.1</td></tr><tr><td>34a33</td><td>Enterobacter ludwigii</td><td>Wheat</td><td>Epoisses</td><td>12,914</td><td>15,383</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4983446</td><td>4881988</td><td>1</td><td>54.48</td><td>30</td><td>SAMN47300691</td><td>SRX27954003</td><td>GCA_050627035.1</td></tr><tr><td>4c6</td><td>Enterobacter ludwigii</td><td>Pea Balltrap</td><td>Epoisses</td><td>24,107</td><td>16,628</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4983447</td><td>4881989</td><td>1</td><td>54.48</td><td>61</td><td>SAMN47300697</td><td>SRX27954009</td><td>GCA_050626925.1</td></tr><tr><td>4b24</td><td>Enterobacter ludwigii</td><td>Pea Balltrap</td><td>Epoisses</td><td>26,176</td><td>16,314</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>4983447</td><td>4881989</td><td>1</td><td>54.48</td><td>65</td><td>SAMN47300698</td><td>SRX27954010</td><td>GCA_050626905.1</td></tr><tr><td>19b38</td><td>Enterobacter mori</td><td>Pea Dexter</td><td>Epoisses</td><td>26,063</td><td>7,611</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>8</td><td>4946610</td><td>4907588</td><td>1</td><td>55.49</td><td>31</td><td>SAMN47300703</td><td>SRX27954016</td><td>GCA_050710095.1</td></tr><tr><td>25c27</td><td>Enterobacter mori</td><td>Pea Dexter</td><td>Auzeville</td><td>26,278</td><td>16,097</td><td>C:100.0%<br/>[S:23.4%,D:76.6%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>4911960</td><td>4911960</td><td>1</td><td>55.48</td><td>66</td><td>SAMN47300683</td><td>SRX27953994</td><td>GCA_050627085.1</td></tr><tr><td>25b30</td><td>Massilia eburnea</td><td>Pea Dexter</td><td>Auzeville</td><td>11,420</td><td>15,370</td><td>C:77.4%<br/>[S:77.4%,D:0.0%]F:2.4%,M:20.2%,n:124</td><td>36</td><td>4594051</td><td>163959</td><td>9</td><td>62.08</td><td>29</td><td>SAMN47300687</td><td>SRX27953998</td><td>GCA_050709955.1</td></tr><tr><td>10c5</td><td>Microbacterium<br/>phylospheaceae</td><td>Pea Balltrap</td><td>Auzeville</td><td>90,071</td><td>14,152</td><td>C:98.4%<br/>[S:98.4%,D:0.0%]F:0.8%,M:0.8%,n:124</td><td>1</td><td>3826298</td><td>3826298</td><td>1</td><td>67.97</td><td>264</td><td>SAMN47300675</td><td>SRX27954022</td><td>GCA_050628115.1</td></tr><tr><td>8b26</td><td>Paenibacillus sp. 8b26</td><td>Pea Balltrap</td><td>Auzeville</td><td>28,221</td><td>18,206</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>6129587</td><td>6129587</td><td>1</td><td>46.44</td><td>62</td><td>SAMN47300680</td><td>SRX27953991</td><td>GCA_050626875.1</td></tr><tr><td>10c25</td><td>Paraburkholderia<br/>fungorum</td><td>Pea Balltrap</td><td>Auzeville</td><td>16,678</td><td>13,402</td><td>C:100.0%<br/>[S:97.6%,D:2.4%]F:0.0%,M:0.0%,n:124</td><td>6</td><td>9355406</td><td>4731166</td><td>1</td><td>61.74</td><td>17</td><td>SAMN47300676</td><td>SRX27954023</td><td>GCA_050710135.1</td></tr></tbody></table>

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<table><caption>TABLE 1 Taxonomic identification, related metadata, HiFi reads statistics, genome assembly statistics (BUSCO with the alphaproteobacteria_odb10 data set and QUAST), and accession numbers for the 38 bacterial whole-genome sequences⁶ (Continued)</caption><thead><tr><th rowspan="2">Strain Code<sup>a</sup></th><th rowspan="2">Taxonomic Affiliation</th><th colspan="2">Metadata</th><th colspan="2">HiFi reads statistics</th><th colspan="5">Genome assembly statistics</th><th colspan="5">Accession numbers</th></tr><tr><th>Plant</th><th>Soil type</th><th>Read counts</th><th>N50 (bp)</th><th>BUSCO Results</th><th># Contigs</th><th>Total Length (bp)</th><th>N50 (bp)</th><th>L50</th><th>GC (%)</th><th>Coverage (x)</th><th>Biosample accession No.</th><th>SRA accession No.</th><th>Assembly accession No.</th></tr></thead><tbody><tr><td>18a25</td><td>Paraburkholderia fungorum</td><td>Pea Dexter</td><td>Epoisses</td><td>24,018</td><td>14,819</td><td>C:100.0%<br/>[S:97.6%,D:2.4%]F:0.0%,M:0.0%,n:124</td><td>4</td><td>9322411</td><td>4729161</td><td>1</td><td>61.73</td><td>28</td><td>SAMN47300704</td><td>SRX27954017</td><td>GCA_050627395.1</td></tr><tr><td>25c37</td><td>Paraburkholderia fungorum</td><td>Pea Dexter</td><td>Auzeville</td><td>19,568</td><td>13,825</td><td>C:100.0%<br/>[S:97.6%,D:2.4%]F:0.0%,M:0.0%,n:124</td><td>4</td><td>9322396</td><td>4729159</td><td>1</td><td>61.73</td><td>21</td><td>SAMN47300686</td><td>SRX27953997</td><td>GCA_050627075.1</td></tr><tr><td>36b22</td><td>Polaromonas aquatica</td><td>Wheat</td><td>Auzeville</td><td>29,313</td><td>8,352</td><td>C:100.0%<br/>[S:99.2%,D:0.8%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>4557853</td><td>4557853</td><td>1</td><td>61.59</td><td>41</td><td>SAMN47300672</td><td>SRX27954001</td><td>GCA_050626995.1</td></tr><tr><td>4a21</td><td>Pseudomonas alvandae</td><td>Pea Balltrap</td><td>Epoisses</td><td>15,580</td><td>14,932</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>6213704</td><td>6213704</td><td>1</td><td>60.96</td><td>27</td><td>SAMN47300699</td><td>SRX27954011</td><td>GCA_050626915.1</td></tr><tr><td>18b10</td><td>Pseudomonas brassicacearum</td><td>Pea Dexter</td><td>Epoisses</td><td>30,999</td><td>9,515</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>6739771</td><td>6739771</td><td>1</td><td>60.87</td><td>33</td><td>SAMN47300705</td><td>SRX27954018</td><td>GCA_050627145.1</td></tr><tr><td>22c22</td><td>Pseudomonas brassicacearum</td><td>Pea Dexter</td><td>Auzeville</td><td>24,495</td><td>9,452</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>2</td><td>6825820</td><td>6816008</td><td>1</td><td>60.81</td><td>25</td><td>SAMN47300688</td><td>SRX27953999</td><td>GCA_050710055.1</td></tr><tr><td>35a7</td><td>Pseudomonas gorinensis</td><td>Wheat</td><td>Epoisses</td><td>73,210</td><td>13,958</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.8%,M:0.0%,n:124</td><td>2</td><td>7145029</td><td>7138193</td><td>1</td><td>60.51</td><td>114</td><td>SAMN47300692</td><td>SRX27954004</td><td>GCA_050709935.1</td></tr><tr><td>21c7</td><td>Pseudomonas gorinensis</td><td>Pea Dexter</td><td>Auzeville</td><td>96,544</td><td>13,640</td><td>C:99.2%<br/>[S:98.4%,D:0.8%]F:0.8%,M:0.0%,n:124</td><td>1</td><td>7207491</td><td>7207491</td><td>1</td><td>60.48</td><td>142</td><td>SAMN47300689</td><td>SRX27954000</td><td>GCA_050627115.1</td></tr><tr><td>34a15</td><td>Pseudomonas gorinensis</td><td>Wheat</td><td>Epoisses</td><td>6,711</td><td>19,431</td><td>C:99.2%<br/>[S:98.4%,D:0.8%]F:0.8%,M:0.0%,n:124</td><td>1</td><td>7206726</td><td>7206726</td><td>1</td><td>60.48</td><td>14</td><td>SAMN47300693</td><td>SRX27954005</td><td>GCA_050627045.1</td></tr><tr><td>9b17</td><td>Pseudomonas simiae</td><td>Pea Balltrap</td><td>Auzeville</td><td>36,437</td><td>8,757</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>2</td><td>6324885</td><td>6316763</td><td>1</td><td>60.28</td><td>39</td><td>SAMN47300677</td><td>SRX27954024</td><td>GCA_050709815.1</td></tr><tr><td>3c1</td><td>Pseudomonas siliginis</td><td>Pea Balltrap</td><td>Epoisses</td><td>113,858</td><td>13,435</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>5970447</td><td>5970447</td><td>1</td><td>60.04</td><td>195</td><td>SAMN47300700</td><td>SRX27954013</td><td>GCA_050626965.1</td></tr><tr><td>25b28</td><td>Pseudomonas solani</td><td>Pea Dexter</td><td>Auzeville</td><td>42,504</td><td>10,604</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.8%,M:0.0%,n:124</td><td>3</td><td>7144013</td><td>3964255</td><td>1</td><td>65.89</td><td>48</td><td>SAMN47300690</td><td>SRX27954002</td><td>GCA_050709975.1</td></tr><tr><td>35c15</td><td>Pseudomonas thivervalensis</td><td>Wheat</td><td>Epoisses</td><td>11,620</td><td>16,943</td><td>C:100.0%<br/>[S:100.0%,D:0.0%]F:0.0%,M:0.0%,n:124</td><td>1</td><td>6495419</td><td>6495419</td><td>1</td><td>61.22</td><td>22</td><td>SAMN47300694</td><td>SRX27954006</td><td>GCA_050627015.1</td></tr><tr><td>8a22</td><td>Pseudomonas thivervalensis</td><td>Pea Balltrap</td><td>Auzeville</td><td>9,214</td><td>12,166</td><td>C:99.2%<br/>[S:99.2%,D:0.0%]F:0.0%,M:0.8%,n:124</td><td>2</td><td>6979370</td><td>5539090</td><td>1</td><td>61.01</td><td>12</td><td>SAMN47300679</td><td>SRX27954026</td><td>GCA_050709855.1</td></tr><tr><td>4a18</td><td>Ralstonia holmesii</td><td>Pea Balltrap</td><td>Epoisses</td><td>5,942</td><td>14,080</td><td>C:98.4%<br/>[S:78.2%,D:3.2%]F:4.0%,M:14.6%,n:124</td><td>4</td><td>5578591</td><td>3593299</td><td>1</td><td>63.58</td><td>12</td><td>SAMN47300701</td><td>SRX27954014</td><td>GCA_050626935.1</td></tr><tr><td>18a19</td><td>Ralstonia insidiosa</td><td>Pea Dexter</td><td>Epoisses</td><td>9,068</td><td>14,820</td><td>C:100.0%<br/>[S:99.2%,D:0.8%]F:0.0%,M:0.0%,n:124</td><td>4</td><td>5999436</td><td>3744346</td><td>1</td><td>63.57</td><td>16</td><td>SAMN47300707</td><td>SRX27954020</td><td>GCA_050627405.1</td></tr><tr><td>18c12</td><td>Ralstonia insidiosa</td><td>Pea Dexter</td><td>Epoisses</td><td>9,113</td><td>14,582</td><td>C:100.0%<br/>[S:99.2%,D:0.8%]F:0.0%,M:0.0%,n:124</td><td>4</td><td>6739771</td><td>6739771</td><td>1</td><td>60.87</td><td>16</td><td>SAMN47300706</td><td>SRX27954019</td><td>GCA_050627135.1</td></tr></tbody></table>

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<table><caption>TABLE 1 Taxonomic identification, related metadata, HiFi reads statistics, genome assembly statistics (BUSCO with the alphaproteobacteria_odb10 data set and QUAST), and accession numbers for the 38 bacterial whole-genome sequences<sup>a</sup> (Continued)</caption><thead><tr><th rowspan="2">Strain Code<sup>b</sup></th><th rowspan="2">Taxonomic Affiliation</th><th colspan="2">Metadata</th><th colspan="2">HiFi reads statistics</th><th colspan="2">Genome assembly statistics</th><th rowspan="2"># Contigs</th><th rowspan="2">Total Length<br>(bp)</th><th rowspan="2">N50 (bp)</th><th rowspan="2">L50</th><th rowspan="2">GC (%)</th><th rowspan="2">Coverage<br>(x)</th><th colspan="2">Accession numbers</th></tr><tr><th>Plant</th><th>Soil type</th><th>Read<br>counts</th><th>N50 (bp)</th><th>BUSCOs Results</th><th>Biosample<br>accession No.</th><th>SRA accession No.</th><th>Assembly accession<br>No.</th></tr></thead><tbody><tr><td>37a14</td><td>Ralstonia thomasi</td><td>Wheat</td><td>Auzeville</td><td>10,129</td><td>15,860</td><td>C:99.2%<br>(S:98.4%,D:0.8%),F:0.8%,M:0.0%,n:124</td><td>3</td><td>5138688</td><td>3497269</td><td>1</td><td>63.80</td><td>23</td><td>SAMN47300674</td><td>SRX27954021</td><td>GCA_050626975.1</td></tr><tr><td>37a16</td><td>Roseateles noduli</td><td>Wheat</td><td>Auzeville</td><td>11,881</td><td>14,537</td><td>C:98.2%<br>(S:24.2%,D:0.0%),F:5.6%,M:70.2%,n:124</td><td>1</td><td>6630955</td><td>6630955</td><td>1</td><td>68.53</td><td>20</td><td>SAMN47300671</td><td>SRX27953990</td><td>GCA_050626985.1</td></tr><tr><td>35b25</td><td>Variolarox paradoxus</td><td>Wheat</td><td>Epoisses</td><td>53,373</td><td>11,279</td><td>C:100.0%<br>(S:100.0%,D:0.0%),F:0.0%,M:0.0%,n:124</td><td>2</td><td>6043317</td><td>556705</td><td>1</td><td>64.82</td><td>76</td><td>SAMN47300695</td><td>SRX27954007</td><td>GCA_050627025.1</td></tr><tr><td>8a8</td><td>Variolarox paradoxus</td><td>Pea Balltrap</td><td>Auzeville</td><td>7,620</td><td>16,223</td><td>C:98.4%<br>(S:98.4%,D:0.0%),F:0.8%,M:0.8%,n:124</td><td>2</td><td>6299093</td><td>5159596</td><td>1</td><td>66.30</td><td>15</td><td>SAMN47300681</td><td>SRX27953992</td><td>GCA_050626895.1</td></tr></tbody></table>

<footnote><sup>a</sup>BUSCO abbreviations; C = Complete, S = Single copy, D = Duplicated, F = Fragmented, M = Missing, n = Number of BUSCO groups searched. Strains are listed in alphabetical order based on their taxonomic affiliation.</footnote>

<footnote><sup>b</sup>Boldface indicates the strain codes in the first column, which are internal laboratory identifiers assigned to each isolate and used throughout the study for traceability purposes.</footnote>
showing an average completeness of 98.85% (range: 77.40% - 100.00%) and average genome size of 6,067,693 bp (range: 3,826,298 bp - 9,355,406 bp). Chromosomes and plasmids were identified using BLAST v2.16.0. Single-contig assemblies were confirmed circular by Flye reports and submitted as complete genomes to NCBI. Taxonomic classification used Kraken2 v2.1.2 (13) and GTDB-Tk v2.4.0 (14). Assembly summaries are in Table 1.

Genome mining with antiSMASH v7.0 (15) identified 203 biosynthetic gene clusters across the 38 strains, linked to 51 putative secondary metabolites. Sixteen distinct siderophore compounds were annotated via the SIDERITE database (16), including alcaligin, enterobactin, aerobactin, pyoverdine, pyochelin, cepaciachelin, staphyloferrin B, malleobactin, variochelin, desferrioxamine, corrugatin, turnerbactin, methanobactin, histicorrugatin, delftibactin, and pacifibactin.

## ACKNOWLEDGMENTS

This research was funded by the EFfORT project – Institut Carnot Plant2Pro. Liya Zhu's PhD was funded by the China Scholarship Council and INRAE France. This work was performed in collaboration with the GeT core facility, Toulouse, France (GeT, https://doi.org/10.15454/1.5572370921303193E12). GeT core facility was supported by France Génomique National infrastructure, funded as part of “Investissement d'avenir” program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09).

The authors thank Amélie Semblat and Jean-Paul Lemaître for their technical assistance in the isolation and selection of the 38 strains.

## AUTHOR AFFILIATIONS

¹Agroécologie, INRAE, Institut Agro, Université Bourgogne Europe, Dijon, France

²INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France

³Université de Pau et des Pays de l'Adour, CNRS, IPREM, E2S UPPA, Pau, France

## AUTHOR ORCIDs

Barbara Pivato http://orcid.org/0000-0003-4500-8834

## FUNDING

<table><thead><tr><th>Funder</th><th>Grant(s)</th><th>Author(s)</th></tr></thead><tbody><tr><td>Institut Carnot Plant2Pro</td><td>EFfORT</td><td>Liya Zhu<br>Céline Lopez-Roques<br>Marine Sallaberry<br>Kory Jason<br>Sylvie Mazurier<br>Barbara Pivato</td></tr><tr><td>China Scholarship Council</td><td></td><td>Liya Zhu</td></tr><tr><td>Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement</td><td></td><td>Liya Zhu</td></tr><tr><td>Agence Nationale de la Recherche</td><td>ANR-10-INBS-09</td><td>Céline Lopez-Roques<br>Marine Sallaberry<br>Kory Jason</td></tr></tbody></table>

## AUTHOR CONTRIBUTIONS

Liya Zhu, Data curation, Formal analysis, Resources, Software, Writing – original draft, Writing – review and editing | Céline Lopez-Roques, Methodology, Writing – review and editing | Marine Sallaberry, Methodology | Kory Jason, Methodology | Laurent Ouerdane, Methodology | Sylvie Mazurier, Writing – review and editing | Philippe Lemanceau,
Conceptualization, Writing – review and editing | Barbara Pivato, Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Writing – review and editing

DATA AVAILABILITY

The complete genome sequence of the 38 siderophore-producing strains have been submitted to NCBI with bioproject ID PRJNA1234539. The scripts used for the assembly quality assessment are available at https://forgemia.inra.fr/Liya_Zhu/effort_38strains.git.

REFERENCES

1. Robin A, Vansuyt G, Hinsinger P, Meyer JM, Briat JF, Lemanceau P. 2008. Chapter 4 Iron dynamics in the rhizosphere, p 183–225. In Advances in agronomy. Elsevier.

2. Lurthy T, Cantat C, Jeudy C, Declerck P, Gallardo K, Barraud C, Leroy F, Ourry A, Lemanceau P, Salon C, Mazurier S. 2020. Impact of bacterial siderophores on iron status and ionome in pea. Front Plant Sci 11:730. https://doi.org/10.3389/fpls.2020.00730

3. Shirley M, Avoscan L, Bernaud E, Vansuyt G, Lemanceau P. 2011. Comparison of iron acquisition from Fe-pyoverdine by strategy I and strategy II plants. Botany 89:731–735. https://doi.org/10.1139/b11-054

4. Vansuyt G, Robin A, Briat J-F, Curie C, Lemanceau P. 2007. Iron acquisition from Fe-pyoverdine by *Arabidopsis thaliana*. Mol Plant Microbe Interact 20:441–447. https://doi.org/10.1094/MPMI-20-4-0441

5. Kramer J, Özkaya Ö, Kümmerli R. 2020. Bacterial siderophores in community and host interactions. Nat Rev Microbiol 18:152–163. https://doi.org/10.1038/s41579-019-0284-4

6. Lemanceau P, Expert D, Gaymard F, Bakker P, Briat J-F. 2009. Chapter 12 Role of iron in plant-microbe interactions, p 491–549. In Advances in botanical research. Academic Press.

7. Semblat A, Turanoglu C, Faivre-Primot C, Lemaître J-P, Marchand D, Dufayet V, Rouet P, Avoscan L, Mazurier S, Lemanceau P, Journet E-P, Pivato B. 2025. Impact of pea-wheat intercropping on grain ionome in relation with changes in *Pseudomonas* spp. and Enterobacterales abundances. Plant Soil 509:261–288. https://doi.org/10.1007/s11104-02-4-06861-x

8. Louden BC, Haarmann D, Lynne AM. 2011. Use of blue agar CAS assay for siderophore detection. J Microbiol Biol Educ 12:51–53. https://doi.org/10.1128/jmb.e12i1.249

9. Arora NK, Verma M. 2017. Modified microplate method for rapid and efficient estimation of siderophore produced by bacteria. 3 Biotech 7:381. https://doi.org/10.1007/s13205-017-1008-y

10. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37:540–546. https://doi.org/10.1038/s41587-019-0072-8

11. Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol 38:4647–4654. https://doi.org/10.1093/molbev/msab199

12. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/btt086

13. Wood DE, Lu J, Langmead B. 2019. Improved metagenomic analysis with Kraken 2. Genome Biol 20:257. https://doi.org/10.1186/s13059-019-1891-0

14. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. 2020. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36:1925–1927. https://doi.org/10.1093/bioinformatics/bt z848

15. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T. 2023. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 51:W46–W50. https://doi.org/10.1093/nar/gkad344

16. He R, Gu S, Xu J, Li X, Chen H, Shao Z, Wang F, Shao J, Yin W-B, Qian L, Wei Z, Li Z. 2024. SIDERITE: Unveiling hidden siderophore diversity in the chemical space through digital exploration. iMeta 3:e192. https://doi.org/10.1002/imt2.192