# Genome Sequences of 17 Strains from Eight Races of Xanthomonas campestris pv. campestris

Caroline Bellenot, Sébastien Carrère, Carine Gris, Laurent Noël, Matthieu Arlat

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Caroline Bellenot, Sébastien Carrère, Carine Gris, Laurent Noël, Matthieu Arlat. Genome Sequences of 17 Strains from Eight Races of Xanthomonas campestris pv. campestris. Microbiology Resource Announcements, 2022, 11 (7), 10.1128/mra.00279-22. hal-03842450

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# Genome Sequences of 17 Strains from Eight Races of *Xanthomonas campestris* pv. *campestris*

Caroline Bellenot,ª,ᵇ,ᶜ Sébastien Carrère,ª,ᵇ,ᶜ Carine Gris,ª,ᵇ,ᶜ Laurent D. Noël,ª,ᵇ,ᶜ Matthieu Arlatª,ᵇ,ᶜ

**ABSTRACT** *Xanthomonas campestris* pv. campestris is a group of phytopathogenic bacteria causing black rot disease on Brassicaceae crops. Here, we report on draft genome sequences of 17 strains representing eight of nine known races of this pathogen, including the pathotype strain CFBP 6865.

Genomic analysis is a powerful approach to study the diversity and evolution of virulence determinants of pathogenic bacteria (1, 2). *Xanthomonas campestris* pv. campestris is the causal agent of black rot disease, affecting many crop plants from the Brassicaceae family (3). *X. campestris* pv. campestris strains have been organized into nine races based on symptoms caused on a set of host and nonhost plants (3). Amplified fragment length polymorphism (AFLP) allowed the classification of *X. campestris* pv. campestris strains into seven genomic clades (clades A to G) (4), which is not congruent with the race classification. Here, we present the genome sequences of 17 *X. campestris* pv. campestris strains (Table 1), including the pathotype strain CFBP 6865. These strains were isolated from different crop varieties or subspecies of *Brassica oleracea* and *Brassica rapa* between 1958 and 2002, in Australia, Belgium, China, France, or Germany. They belong to four of the seven genomic clades and are representative of eight of the nine known races. All of these strains were obtained from the International Centre for Microbial Resources-French Collection for Plant-Associated Bacteria (CIRM-CFBP), National Research Institute for Agriculture, Food, and the Environment (INRAE).

The *X. campestris* pv. campestris strains were grown overnight in MOKA-rich medium (4 g/L yeast extract, 8 g/L Casamino Acids, 2 g/L K₂HPO₄, and 0.3 g/L MgSO₄·7H₂O) at 28°C. From these cultures, genomic DNA was extracted with a Wizard genomic DNA purification kit (Promega). Genomic DNA libraries were prepared using a NEXTflex PCR-free DNA-sequencing kit (PerkinElmer) for most strains and a NEBNext kit (New England BioLabs) for strains CFBP 119, CFBP 4953, CFBP 4956, CFBP 6863, CN19, and CN20. All libraries were constructed following the manufacturers' instructions. *X. campestris* pv. campestris total genomic DNA (including chromosome and plasmids) was sequenced on an Illumina HiSeq 2000 platform (2 × 101-bp paired-end reads) or a Genome Analyzer IIx system (2 × 76-bp paired-end reads) (for strains CFBP 119, CFBP 4953, CFBP 4956, CFBP 6863, CN19, and CN20). Several assemblies were produced using the SOAPdenovo assembler (5) with incremental *k*-mer sizes (starting with a *k*-mer length corresponding to one-third of the read length, to a maximum of 99 nucleotides [nt], with a step of 4 nt). The resulting contigs were scaffolded using the Velvet assembler (6) (parameters: -cov_cutoff 5 -min_contig_length 100 -max_divergence 0.05 -exportFiltered yes -exp_cov auto) using the same *k*-mer range. A final round with SOAPGapCloser (parameter: -p 31) was performed to fill in the gaps, and the remaining redundancy (misassembled contigs) was removed using MegaBLAST-based identification. Genome sequences were annotated using the default parameters of the EuGene-P annotation pipeline to identify RNAs and protein-coding genes (7). The completeness of the genomes was assessed with BUSCO v5.1.2 (default parameters), using the xanthomonadales_odb10 data set (8, 9) (Table 1).

**Editor** David A. Baltrus, University of Arizona

**Copyright** © 2022 Bellenot et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Matthieu Arlat, matthieu.arlat@inrae.fr.

The authors declare no conflict of interest.

**Received** 18 March 2022

**Accepted** 16 May 2022

**Published** 13 June 2022

<footnote>ªINRAE, UMR 441, Laboratoire des Interactions Plantes-Microbes-Environnement, Castanet-Tolosan, France</footnote>

<footnote>ᵇCNRS, UMR 2594, Laboratoire des Interactions Plantes-Microbes-Environnement, Castanet-Tolosan, France</footnote>

<footnote>ᶜUniversité de Toulouse, Université Paul Sabatier, Toulouse, France</footnote>
<table><caption>TABLE 1 Description of the Xanthomonas campestris pv. campestris strains reported and statistics for the sequencing and assembly of their genomes</caption><thead><tr><th>Strain</th><th>CFBP designation<sup>a</sup></th><th>Clade<sup>b</sup></th><th>Ra</th><th>Date of isolation</th><th>Host</th><th>Country of isolation</th><th>No. of rea ds</th><th>Genome size (bp) (x)</th><th>Genome coverage (x)</th><th>No. of contigs</th><th>N<sub>iso</sub> (bp)</th><th>GC content (%)</th><th>BUSCO completeness (%)</th><th>No. of coding sequences</th><th>GenBank accession no.</th><th>SRA accession no.</th><th>DOI no.</th></tr></thead><tbody><tr><td>147</td><td>CFBP 7156</td><td>A</td><td>4</td><td>1967</td><td>Brassica oleracea var. botrytis</td><td>France</td><td>10,035,656</td><td>5,060,825</td><td>320</td><td>141</td><td>80,681</td><td>65.0</td><td>99.9</td><td>4,305</td><td>AVE000000000.1/</td><td>SRP322641</td><td>10.25794/reference/um8naue7</td></tr><tr><td>CFBP 1119</td><td>CFBP 1119</td><td>C</td><td>8</td><td>1967</td><td>Brassica oleracea var. botrytis</td><td>France</td><td>35,046,928</td><td>5,008,837</td><td>1,063</td><td>74</td><td>183,459</td><td>64.6</td><td>99.9</td><td>4,220</td><td>CBVE000000000.1/</td><td>SRP322638</td><td>10.25794/reference/njwm710</td></tr><tr><td>CFBP 1124</td><td>CFBP 1124</td><td>E</td><td>5</td><td>1975</td><td>Brassica oleracea var. Capitata</td><td>France</td><td>7,211,603</td><td>4,997,962</td><td>240</td><td>103</td><td>149,591</td><td>65.6</td><td>99.7</td><td>4,436</td><td>AVE000000000.1/</td><td>SRP322639</td><td>10.25794/reference/yihylqnob</td></tr><tr><td>CFBP 1712</td><td>CFBP 1712</td><td>E</td><td>5</td><td>1975</td><td>Brassica oleracea var. botrytis</td><td>France</td><td>17,215,274</td><td>5,015,961</td><td>553</td><td>129</td><td>79,498</td><td>64.9</td><td>98.6</td><td>4,461</td><td>AVDC000000000.1/</td><td>SRP322649</td><td>10.25794/reference/dnvsf18</td></tr><tr><td>CFBP 1713</td><td>CFBP 1713</td><td>E</td><td>5</td><td>1975</td><td>Brassica oleracea var. botrytis</td><td>France</td><td>18,408,662</td><td>5,041,610</td><td>739</td><td>89</td><td>151,632</td><td>64.4</td><td>99.4</td><td>4,491</td><td>AVDF000000000.1/</td><td>SRP322642</td><td>10.25794/reference/rmbgely</td></tr><tr><td>CFBP 4953</td><td>CFBP 4953</td><td></td><td>7</td><td>1999</td><td>Brassica oleracea var. botrytis cv. Cortes</td><td>Belgium</td><td>32,918,799</td><td>5,052,992</td><td>991</td><td>83</td><td>163,533</td><td>64.7</td><td>99.9</td><td>4,562</td><td>CBVF000000000.1/</td><td>SRP322648</td><td>10.25794/reference/nmnw_mqq</td></tr><tr><td>CFBP 4954</td><td>CFBP 4954</td><td></td><td>6</td><td>1999</td><td>Brassica oleracea var. botrytis cv. Aviso</td><td>Belgium</td><td>6,433,757</td><td>5,073,734</td><td>204</td><td>149</td><td>66,639</td><td>65.1</td><td>99.4</td><td>4,496</td><td>AVDE00000000.1/</td><td>SRP322643</td><td>10.25794/reference/fxlurkw</td></tr><tr><td>CFBP 4955</td><td>CFBP 4955</td><td>E</td><td>9</td><td>1999</td><td>Brassica oleracea var. botrytis cv. Aviso</td><td>Belgium</td><td>4,239,839</td><td>5,136,167</td><td>138</td><td>142</td><td>84,609</td><td>65.1</td><td>99.7</td><td>4,600</td><td>AVDF00000000.1/</td><td>SRP322645</td><td>10.25794/reference/cd2vneut</td></tr><tr><td>CFBP 4956</td><td>CFBP 4956</td><td></td><td>4</td><td>1999</td><td>Brassica oleracea var. botrytis cv. Spacestar</td><td>Belgium</td><td>37,480,089</td><td>4,965,880</td><td>1,148</td><td>125</td><td>109,963</td><td>64.5</td><td>99.8</td><td>4,396</td><td>CBVG000000000.1/</td><td>SRP322646</td><td>10.25794/reference/rx9gmcmt</td></tr><tr><td>CFBP 5130</td><td>CFBP 5130</td><td>A</td><td>7</td><td>1979</td><td>Brassica sp.</td><td>France</td><td>9,232,935</td><td>5,056,538</td><td>295</td><td>129</td><td>93,783</td><td>64.9</td><td>99.7</td><td>4,561</td><td>AVDG000000000.1/</td><td>SRP322647</td><td>10.25794/reference/_01691q</td></tr><tr><td>CFBP 5683</td><td>CFBP 5683</td><td>E</td><td>3</td><td>1958</td><td>Brassica oleracea var. botrytis</td><td>France</td><td>2,579,478</td><td>5,030,566</td><td>82</td><td>184</td><td>51,279</td><td>65.4</td><td>98.8</td><td>4,492</td><td>AVDH000000000.1/</td><td>SRP322644</td><td>10.25794/reference/osr1ne3k</td></tr><tr><td>CFBP 6863</td><td>CFBP 6863</td><td></td><td>9</td><td></td><td>Brassica oleracea var. botrytis</td><td>Germany</td><td>32,059,044</td><td>5,001,025</td><td>975</td><td>94</td><td>173,153</td><td>64.5</td><td>99.7</td><td>4,458</td><td>CBVH000000000.1/</td><td>SRP322661</td><td>10.25794/reference/shkh_1dj</td></tr><tr><td>CFBP 6865R<sup>d</sup></td><td>CFBP 6865</td><td></td><td>5</td><td>1975</td><td>Brassica oleracea var. Australia</td><td>Australia</td><td>16,397,066</td><td>5,166,940</td><td>916</td><td>24</td><td>415,646</td><td>63.7</td><td>99.6</td><td>4,657</td><td>AVDT000000000.1/</td><td>SRX11066177</td><td>10.25794/reference/uce572l</td></tr><tr><td>CN01</td><td>CFBP 8237</td><td>A</td><td>1</td><td>2002</td><td>Brassica rapa subsp. pekinensis</td><td>China</td><td>20,801,984</td><td>5,030,897</td><td>836</td><td>75</td><td>179,901</td><td>64.3</td><td>99.9</td><td>4,543</td><td>AVDN000000000.1/</td><td>SRP322694</td><td>10.25794/reference/zzeltq6q</td></tr><tr><td>CN10</td><td>CFBP 8244</td><td>B</td><td>7</td><td>2002</td><td>Brassica rapa subsp. pekinensis</td><td>China</td><td>19,211,549</td><td>4,958,955</td><td>784</td><td>101</td><td>124,175</td><td>64.5</td><td>99.5</td><td>4,411</td><td>AVDR000000000.1/</td><td>SRP322708</td><td>10.25794/reference/h5nghmsn</td></tr><tr><td>CN19</td><td>CFBP 8251</td><td>B</td><td>4</td><td>2002</td><td>Brassica oleracea var. alboglabra</td><td>China</td><td>32,316,246</td><td>4,958,083</td><td>992</td><td>113</td><td>115,047</td><td>64.4</td><td>99.5</td><td>4,422</td><td>CBVC000000000.1/</td><td>SRP322706</td><td>10.25794/reference/e220luq</td></tr><tr><td>CN20</td><td></td><td></td><td></td><td></td><td></td><td></td><td>31,554,774</td><td>5,084,276</td><td>944</td><td>115</td><td>116,198</td><td>64.5</td><td>99.6</td><td>4,551</td><td>CBVD000000000.1/</td><td>SRP322707</td><td>10.25794/reference/e3ex38nh</td></tr></tbody></table>

<sup>a</sup> Strains are available in the CIRM-CFBP (www.cirm-cfbp.fr/page/Home).

<sup>b</sup> Clades based on AFLP of X. campestris pv. campestris strains reported by Guy et al. (4).

<sup>c</sup> Races as described previously by Vicente and Holub (3).

<sup>d</sup> Pathotype strain.
**Data availability.** The genome sequences were deposited in GenBank, and the raw reads were deposited in the Sequence Read Archive (SRA); their accession numbers are listed in Table 1. The genome annotations are available under the DOI numbers provided in Table 1.

## ACKNOWLEDGMENTS

We acknowledge the CIRM-CFBP for providing the strains. We are grateful to Perrine David (HM Clause, France) for the race typing of *X. campestris* pv. campestris strains performed in the framework of the Brassichax project (Limagrain).

C.B. was funded by a PhD grant from the ANR NEPHRON (grant ANR-18-CE20-0020-01) and CNRS. S.C., C.G., L.D.N., and M.A. were supported by the ANR XANTHOMIX (grant ANR-2010-GENM-013-02) and NEPHRON (grant ANR-18-CE20-0020-01). This study is set within the frameworks of the Laboratoires d'Excellences (LABEX) TULIP (ANR-10-LABX-41) and of the École Universitaire de Recherche (EUR) TULIP-GS (ANR-18-EURE-0019).

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