# Complete and nearly complete genome sequences of seven strains of *Burkholderia glumae* and *B. gladioli* isolated from rice panicles in Vietnam

Doan Thi Kieu Tien,¹ Van Quoc Giang,¹ Pham Van Luc,¹ Kha Thi Tuong Vy,¹ Huynh Thi Thong,¹ Lam Van Hau,¹ Pierre Lefeuvre,² Nguyen Thi Thu Nga¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 4.

**ABSTRACT** *Burkholderia gladioli* and *Burkholderia glumae* are two of the main pathogens associated with bacterial panicle blight, a major disease of rice worldwide. Here, we present complete and nearly complete genome assemblies of three *B. glumae* and four *B. gladioli* strains isolated from rice collected in the Mekong Delta area.

**KEYWORDS** *Burkholderia*, bacterial panicle blight, Vietnam

Bacterial panicle blight (BPB) is a globally destructive disease of rice (1) primarily associated with *Burkholderia glumae* (2) and *Burkholderia gladioli* (3). In Vietnam, BPB is recognized as a constraint to rice production in all production areas (4, 5), but knowledge of the bacterial diversity in the country is limited to only 16S sequences of *B. glumae* and *B. gladioli* and a single draft genome of *B. glumae* available in the database.

In order to gain knowledge on the diversity of bacteria potentially associated with the disease in the country, panicles showing symptoms of BPB were sampled from seven rice fields in the Mekong Delta area from May to July 2024 (Table 1). Panicles were washed with 70% EtOH, cut into small pieces using scalpels, and ground with a glass rod in 50 µL of water. Products were streaked on King's B medium plates (6) before incubation at 25°C for 2–3 days. Round colonies of 1–2 mm diameters that released yellow pigment were cultured in 5 mL King's Medium B Broth for 24 h at 25°C and 120 rpm/min (titer of ~10⁸ CFU/mL) before genomic DNA extraction using the Monarch Spin gDNA Extraction Kit (NEB). Long-read Oxford Nanopore MinION sequencing was performed in multiplex on a FLO-MIN114 flow cell using the SQK-RBK114-24 kit for library preparation and following the manufacturer's instructions. Default parameters were used for all software unless otherwise noted. Super-accurate baseCALLing of raw sequencing signal was performed using Dorado version 0.7.2 (https://github.com/nanoporetech/dorado) with a minimum mean read PHRED quality score cut off of 8 (Table 1). Reads were used for *de novo* assemblies with Canu version 2.2 (7), specifying a genome size of 6.5 Mb. Contigs flagged as circular from Canu analysis were trimmed using genome coordinates defined by the software. After polishing the assemblies using Medaka version 2.0.0a2 (https://github.com/nanoporetech/medaka), the contigs were annotated using NCBI PGAP version 6.9 (8). Full-length 16S rRNA gene sequences were obtained from the PGAP annotation and were used to validate the *Burkholderia* genus classification using the RDP classifier version 2.14 and associated database (9). Further analysis using Mash version 2.1.1 (10) and the genome reference sequences classified in the *Burkholderia* genus as obtained from NCBI on 23 January 2025 confirmed that strains were isolates of *B. glumae* and *B. gladioli* (Table 1).

All *B. gladioli* assemblies comprised two closed circular chromosomal sequences. *B. glumae* strains presented with a single circular chromosomal sequence and one to two

**Editor** Leighton Pritchard, University of Strathclyde,
Glasgow, United Kingdom

Address correspondence to Pierre Lefeuvre,
pierre.lefeuvre@cirad.fr.

The authors declare no conflict of interest.

See the funding table on p. 4.

Received 21 April 2025

Accepted 3 June 2025

Published 18 June 2025

Copyright © 2025 Tien 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 Strain details and summary of assembly statistics</caption><thead><tr><th>Strain</th><th>Collection date</th><th>Sampling location</th><th>Sampling latitude and longitude</th><th>SRA</th><th>Total reads (total Mb)</th><th>Reads N50 length (bp)</th><th>Species (most similar strain/1 – MASH distance)</th><th>Total No. of genes (No. of CDs with protein)</th><th>Sequence accession number</th><th>Length (nt)</th><th>Coverage</th><th>Circular</th><th>Type</th><th>G + C content (%)</th></tr></thead><tbody><tr><td>HG_1</td><td>11-06-2024</td><td>Vietnam: Hau Giang province</td><td>9.68880152 N 105.61437308 E</td><td>SRX27652183</td><td>57,968 (465.8 Mb)</td><td>19,202</td><td>8,231,763 gladioli (BBB-01/0.980)</td><td>7,339 (6.727)</td><td>CP183180.1 4,163,892</td><td>57</td><td>Yes</td><td>Yes</td><td>Chromosome</td><td>0.677</td></tr><tr><td>HG_2</td><td>11-06-2024</td><td>Vietnam: Hau Giang province</td><td>9.68880152 N 105.61437308 E</td><td>SRX27652184</td><td>14,399 (217.0 Mb)</td><td>30,003</td><td>8,231,327 gladioli (BBB-01/0.981)</td><td>7,271 (7,001)</td><td>CP183179.1 3,834,718</td><td>53</td><td>Yes</td><td>Yes</td><td>Chromosome</td><td>0.684</td></tr><tr><td>HG_3</td><td>11-06-2024</td><td>Vietnam: Hau Giang province</td><td>9.68880152 N 105.61437308 E</td><td>SRX27652187</td><td>116,451 (213.4 Mb)</td><td>3,366</td><td>6,824,497 glumae (ATCC 33617/0.993)</td><td>6,145 (5.602)</td><td>CP183177.1 4,163,675</td><td>27</td><td>Yes</td><td>Yes</td><td>Chromosome</td><td>0.677</td></tr><tr><td>HG_4</td><td>11-06-2024</td><td>Vietnam: Hau Giang province</td><td>9.68880152 N 105.61437308 E</td><td>SRX27652185</td><td>64,234 (610.0 Mb)</td><td>19,939</td><td>8,231,748 gladioli (BBB-01/0.980)</td><td>7,348 (6.758)</td><td>CP183174.1 4,163,675</td><td>35,914</td><td>31</td><td>Yes</td><td>Yes</td><td>Chromosome</td><td>0.684</td></tr><tr><td>HG_5</td><td>27-05-2024</td><td>Vietnam: Hau Giang province</td><td>9.96656307 N 105.59525536 E</td><td>SRX27652186</td><td>12,751 (206.5 Mb)</td><td>31,974</td><td>8,231,303 gladioli (BBB-01/0.981)</td><td>7,277 (7,019)</td><td>CP183172.1 178,381</td><td>75</td><td>Yes</td><td>Yes</td><td>Plasmid</td><td>0.635</td></tr><tr><td>HG_7</td><td>27-05-2024</td><td>Vietnam: Hau Giang province</td><td>9.96656307 N 105.59525536 E</td><td>SRX27652188</td><td>121,960 (345.7 Mb)</td><td>6,301</td><td>6,810,121 glumae (ATCC 33617/0.995)</td><td>6,108 (5.611)</td><td>CP183171.1 54,781</td><td>58</td><td>Yes</td><td>Yes</td><td>Plasmid</td><td>0.635</td></tr></tbody></table>

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<table><caption>TABLE 1 Strain details and summary of assembly statistics (Continued)</caption><thead><tr><th>Strain</th><th>Collection date</th><th>Sampling location</th><th>Sampling latitude and longitude</th><th>SRA</th><th>Total reads (total Mb)</th><th>Reads N50 Assembly length (bp)</th><th>Species (most similar strain/1 – MASH distance)</th><th>Total No. of genes (No. of CDs with protein)</th><th>Sequence accession number</th><th>Length (nt)</th><th>Coverage</th><th>Circular</th><th>Type</th><th>G + C content (%)</th></tr></thead><tbody><tr><td rowspan="10">LA_B1</td><td rowspan="10">20-07-2024</td><td rowspan="10">Vietnam: Long An province</td><td rowspan="10">10.74514622 N 105.69122389 E</td><td rowspan="10">SRX27652189</td><td rowspan="10">13,222 (104.4 Mb)</td><td rowspan="10">15,884</td><td rowspan="10">6,919,044</td><td rowspan="10">Burkholderia glumae (ATCC 33617/0.997)</td><td>JBMJCR0100000 3,590,963</td><td>31</td><td>No</td><td>Chromosome</td><td>0.682</td></tr><tr><td>03.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCR0100000 129,652</td><td>28</td><td>No</td><td>Plasmid</td><td>0.615</td></tr><tr><td>05.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCR0100000 110,996</td><td>29</td><td>Yes</td><td>Plasmid</td><td>0.639</td></tr><tr><td>04.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCR0100000 87,757</td><td>38</td><td>No</td><td>Plasmid</td><td>0.615</td></tr><tr><td>02.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCCQ010000 3,565,893</td><td>15</td><td>Yes</td><td>Chromosome</td><td>0.684</td></tr><tr><td>003.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCCQ010000 2,932,420</td><td>15</td><td>No</td><td>Chromosome</td><td>0.684</td></tr><tr><td>001.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCCQ010000 245,243</td><td>15</td><td>Yes</td><td>Plasmid</td><td>0.636</td></tr><tr><td>004.1</td><td></td><td></td><td></td></tr><tr><td>JBMJCCQ010000 175,488</td><td>12</td><td>No</td><td>Plasmid</td><td>0.608</td></tr><tr><td>002.1</td><td></td><td></td><td></td></tr></tbody></table>
contigs that failed to be circularized for the other chromosome. One or two closed plasmids were obtained per strain (54,767-245,243 bp). Six additional uncircularized contigs of 12.4-175.5 kb were obtained and were assigned to plasmids based on online BLASTn (11) searches against the NCBI nr database. Totals of 6,108-7,348 genes were predicted, and completeness of the representative gene set was reported for all genomes using BUSCO version 5.8.0 (12). All strains possessed predicted tetracycline and benzalkonium chloride resistance genes carried on the chromosome, as detected using the online Resistance Gene Identifier server (13).

ACKNOWLEDGMENTS

The European Regional Development Fund (ERDF; contract number GURDT I2016-1731-0006632), the Réunion Region, and CIRAD provided financial support.

AUTHOR AFFILIATIONS

¹College of Agriculture, Can Tho University, Can Tho, Vietnam

²CIRAD, UMR PVBMT, College of Agriculture, Can Tho University, Can Tho, Vietnam

AUTHOR ORCIDs

Pierre Lefeuvre http://orcid.org/0000-0003-2645-8098

FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s)</td><td>Author(s)</td></tr></thead><tbody><tr><td>European Regional Development Fund</td><td>GURDT I2016-1731-0006632</td><td>Pierre Lefeuvre</td></tr><tr><td>Conseil Régional de La Réunion</td><td></td><td>Pierre Lefeuvre</td></tr><tr><td>Centre de Coopération Internationale en Recherche Agronomique pour le Développement</td><td></td><td>Pierre Lefeuvre</td></tr></tbody></table>

DATA AVAILABILITY STATEMENT

The raw data are available under BioProject accession PRJNA1222096.

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