# Whole-genome sequences of *Bipolaris bicolor*, *Curvularia hawaiiensis*, *Curvularia spicifera*, and *Exserohilum rostratum* isolated from rice in Burkina Faso, France, Mali, and Pakistan

Kouka Hilaire Kaboré,¹,² Abalo Itolou Kassankogno,³ Henri Adreit,²,⁴ Sebastien Ravel,²,⁴ Florian Charriat,²,⁴ Diariatou Diagne,⁵
Marc-Henri Lebrun,¹ Didier Tharreau²,⁴

**AUTHOR AFFILIATIONS** See affiliation list on p. 3.

**ABSTRACT** Different fungal species of the *Pleosporaceae* family infect rice, causing similar symptoms. Reference genomic sequences are useful tools to study the evolution of these species and to develop accurate molecular diagnostic tools. Here, we report the complete genome sequences of *Bipolaris bicolor*, *Curvularia hawaiiensis*, *Curvularia spicifera*, and *Exserohilum rostratum*.

**KEYWORDS** phytopathology, rice disease, fungi, population genetics, diagnostic tools, genotypic identification, molecular detection, rice brown spot, genomics, pathogenesis

Rice is a worldwide crop widely consumed in Asia and Africa. Many diseases affect rice production, with an estimated annual loss of 20% in yield (1). Different fungal species infect rice (2), some of which are not sufficiently well studied, in particular, fungi responsible for the rice brown spot diseases, *Bipolaris bicolor*, *Curvularia hawaiiensis*, *Curvularia spicifera*, and *Exserohilum rostratum* (3, 4). In the perspective of developing molecular diagnostic markers, the availability of their complete genomes is essential (5). In 2018, rice seeds and leaves with typical brown spot disease symptoms were collected in rice fields in Burkina Faso, France, Mali, and Pakistan. They were incubated for 5 to 7 days on wet filter paper at 25°C with a 12-h photoperiod. One conidium was isolated from each sample, giving rise to monospore isolates. Genomic DNAs extracted from these isolates were used to amplify glyceraldehyde-3-phosphate dehydrogenase and translation elongation factor 1 alpha (TEF1-a) genes using the primers GPD1/GPD2 (6) and TEF1-983/TEF1-2218 (7), respectively. These PCR products were sequenced, and the alignments of these sequences with sequences in databases showed a 100% identity to reference sequences from *B. bicolor*, *C. hawaiiensis*, *C. spicifera*, and *E. rostratum*, respectively, for the strains ML9021, PK9021, FR9030, and BF9006. Sequences were deposited in NCBI GenBank under accession numbers OP554702, OP554633, OP473603, OP473604, OP473605, OP554576, OP554691, and OP473583. For whole-genome sequencing, each isolate was cultured for 7 days at 25°C (12 h photoperiod) using the Corn Meat Agar (18 g/L) medium previously covered with a sterile cellophane disc. DNA was extracted using approximately 60 mg of fresh mycelium using the cetyl trimethyl ammonium bromide method (8). The genomic library was prepared using the TruSeq Nano DNA library preparation kit from Illumina. Pair-end sequencing (2 × 150 pb) was performed with an Illumina NovaSeq 6000, with an average depth of 50×. The demultiplexing and the production of the fastq files were performed using the bcl2fastq software v2.20.0.422. The quality of sequencing reads was determined using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq-screen/) especially for contaminant detection. Assembly was performed with ABySS software

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

Address correspondence to Kouka Hilaire Kaboré,
koukas2@yahoo.fr.

The authors declare no conflict of interest.

**Received** 22 February 2023

**Accepted** 23 August 2023

**Published** 9 October 2023

Copyright © 2023 Kaboré 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 General features of the complete genome sequences of *B. bicolor*, *C. hawaiiensis*, *C. spicifera*, and *E. rostratum* isolated from rice</caption><thead><tr><th colspan="2">Sequencing</th><th colspan="4">Assembly</th><th colspan="4">BUSCO analysis</th></tr><tr><th>Strains</th><th>Coverage depth (x)</th><th>No. of scaffolds</th><th>Size (bp)</th><th>GC %</th><th>N<sub>50</sub> (bp)</th><th>% of complete</th><th>% of complete and single copy</th><th>% of complete and duplicated</th><th>% of missing</th></tr></thead><tbody><tr><td><i>B. bicolor</i> strain ML9021</td><td>62.9</td><td>218</td><td>35,093,885</td><td>49.14</td><td>965,787</td><td>95.45</td><td>95.38</td><td>0.07</td><td>4.12</td></tr><tr><td><i>C. hawaiiensis</i> strain PK9021</td><td>205.5</td><td>412</td><td>30,043,159</td><td>51.17</td><td>179,076</td><td>94.28</td><td>92.82</td><td>1.46</td><td>5.10</td></tr><tr><td><i>C. spicifera</i> strain FR9030</td><td>69.4</td><td>171</td><td>31,738,811</td><td>50.98</td><td>745,506</td><td>94.85</td><td>94.64</td><td>0.21</td><td>4.80</td></tr><tr><td><i>E. rostratum</i> strain BF9006</td><td>74</td><td>99</td><td>34,670,870</td><td>50.70</td><td>1,163,278</td><td>94.60</td><td>94.40</td><td>0.21</td><td>4.94</td></tr></tbody></table>

v2.2.1 (9) for different kmer values, and genome completeness was evaluated using BUSCO v5.4.3 with the Pleosporales lineage data set (6,641 genes) (10).

<figure><img src="image_1.png" /><figcaption>FIG 1 Dot plot analysis for genome comparison of *E. rostratum* strains BF9006 and SR-KPL1 using D-GENIES (13). BF9006 as a target is on the x-axis, and SR-KPL1 as a query is on the y-axis. Genomic alignment regions are presented as four-colored lines, corresponding to different similarity values (Yellow: <25% similarity, Orange: 25–50% similarity, Green: 50–75% similarity, and Dark Green: >75%). The long stretches of dark green lines in the diagonal indicate high nucleotide similarity between the two strains of *E. rostratum*.</figcaption></figure>
Total genome lengths ranged from 30 to 35 Mb, the number of scaffolds ranged from 99 to 412, and GC content ranged from 49.14 to 51.17% (Table 1). The BUSCO evaluation showed that the assembly recovered over 93% of the expected single-copy genes in the Pleosporales order. Compared to the *E. rostratum* genome of strain SR-KPL1 isolated from rice in India (11), strain BF9006 described in this study has fewer scaffolds (99 versus 769) and a larger N50 value (340,895 versus 122,824 bp) attesting data quality. The average nucleotide identity (ANI) analysis of the two complete genomes performed using pyani v0.2.11 (12) showed a similarity of 98.32%. Visualization of the alignment of the two genomes (Fig. 1) using D-GENIES v1.5.0 (13) corroborates the high ANI values.

## ACKNOWLEDGMENTS

This work was financially supported by the RICE CRP and the Islamic Development Bank.

We thank Dr. Sajid Ali (The University of Agriculture Peshawar, Pakistan) for providing us with the rice sample from Pakistan. We also thank the Montpellier GenomiX (MGX) platform for sequencing our genomes.

## AUTHOR AFFILIATIONS

## AUTHOR ORCIDs

Kouka Hilaire Kaboré http://orcid.org/0000-0003-1318-6345

Sebastien Ravel https://orcid.org/0000-0001-6663-782X

Didier Tharreau http://orcid.org/0000-0003-3961-6120

## AUTHOR CONTRIBUTIONS

Kouka Hilaire Kaboré, Conceptualization, Data curation, Formal analysis, Methodology, Writing – original draft | Abalo Itolou Kassankogno, Resources, Validation, Writing – original draft | Henri Adreit, Data curation, Methodology, Validation, Writing – original draft | Sebastien Ravel, Data curation, Formal analysis, Methodology, Software, Validation, Writing – original draft | Florian Charriat, Data curation, Formal analysis, Methodology, Software, Validation, Writing – original draft | Diariatou Diagne, Data curation, Investigation, Methodology, Resources, Validation, Writing – original draft | Marc-Henri Lebrun, Investigation, Methodology, Project administration, Resources, Validation, Writing – original draft | Didier Tharreau, Conceptualization, Investigation, Methodology, Project administration, Resources, Validation, Writing – original draft, Funding acquisition, Supervision

## DATA AVAILABILITY

Whole-genome sequences were deposited in NCBI/GenBank under accession numbers **JAODYD000000000**, **JAODYC000000000**, **JAODYB000000000**, and **JANXEY000000000**. The raw data were deposited in the NCBI Sequence Read Archive (SRA) under SRA accession number **SRR23346300**, **SRR23346299**, **SRR23346298**, and **SRR22883102**.

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