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Complete genome sequence of Fusarium kyushuense WFK101 isolated from Vulpia myuros near a rice field in Korea
Korean J. Microbiol. 2024;60(1):41-43
Published online March 31, 2024
© 2024 The Microbiological Society of Korea.

Jae Yun Lim and Jeong-Ah Seo*

School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
Correspondence to: *E-mail: sja815@ssu.ac.kr;
Tel.: +82-2-820-0449; Fax: +82-2-824-4383
Received December 21, 2023; Accepted January 15, 2024.
Abstract
Fusarium kyushuense WFK101 was isolated from Vulpia myuros collected near a rice field in South Korea. Whole genome of F. kyushuense WFK101 was sequenced using the Illumina HiSeq 2500 platform and confirmed to consist of four chromosomes. As a result of the analysis of the average nucleotide identity between F. kyushuense WFK101 and the reference species of the Fusarium sambucinum species complex, it showed the highest similarity of 98.8% with F. kyushuense NRRL 25348. Fusarium kyushuense WFK101 has 47 secondary metabolite gene clusters, and the Tri16 gene was found next to the Tri1 gene on chromosome 1. The genomic information of F. kyushuense WFK101 provides in-depth genetic information about F. kyushuense, which synthesizes the most poisonous type A trichothecene.
Keywords : Fusarium kyushuense, complete genome sequence, Illumina HiSeq, phylogenetic analysis, type A trichothecene
Body

Fusarium kyushuense, one of the Fusarium sambucinum species complex (FSSP), can cause plant diseases and produce type A trichothecene in kernels (Aoki and O’Donnell, 1998). Type A trichothecene is the most concerned Fusarium trichothecene due to its contamination of agricultural products and high toxicity to humans and animals (Mahato et al., 2022). The genetic variations of the Tri1 gene and Tri16 gene of Fusarium strains are known to determine type A trichothecene production (Wang et al., 2023). In our previous study, we obtained F. kyushuense WFK101 from gramineous weed Vulpia myuros collected near the rice field in Boseong, South Korea (Ahn et al., 2022). Since F. kyushuense is a threatening fungal plant pathogen that can produce type A trichothecenes, the genome of F. kyushuense WFK101 was sequenced.

Fusarium kyushuense WFK101 was grown on 5 ml of potato dextrose broth at 25°C for 3 days under shaking condition (180 rpm). A modified CTAB method (Cota-Sánchez et al., 2006) was used to get the genomic DNA of F. kyushuense WFK101 from the culture. The whole genome sequencing of F. kyushuense WFK101 was performed using an Illumina HiSeq 2500 platform and a paired-end strategy (Illumina). On average, 112 times as many Illumina reads were used, and 127 contigs were made using SPAdes assembler v3.14.1 (Prjibelski et al., 2020) for de novo assembly. By using the reference sequence of F. asiaticum KCTC 16664 (GCA_025258505.1; Jeong et al., 2023), 49 contigs were joined together to make 8 contigs. These were then aligned to four chromosomes of F. asiaticum KCTC 16664, with one gap near the centromeric region of each (Table 1, Fig. 1A). Among the remaining contigs, 101 were excluded from further analysis due to mitochondrial DNA, or a short size less than 500 bp. The remaining 14 unplaced contigs totaled around 64 kb.

Draft genome feature of Fusarium kyushuense WFK101 compared with Fusarium kyushuense NRRL 25348

Features Fusarium kyushuense

WFK101 NRRL 25348*
Genome size, bp 36,557,249 36,015,118
GC content, % 47.4 47.7
Number of contigs 22 325
N50, bp 7,019,575 251,145
Number of protein-coding genes 11,964 11,588
Number of InterPro 9,384 9,141
Number of secondary metabolite gene clusters 47 47
BUSCO completeness, % 99.02 97.49
GenBank accession number JAWRWB000000000 JABCJU000000000

*Note: The genome sequence of F. kyushuense NRRL 25348 was obtained from GenBank.



Fig. 1. Genome synteny and phylogenetic analysis of F. kyushuense WFK101. (A) Synteny plot of the chromosomes of F. kyushuense WFK101 and F. asiaticum KCTC 16664 was created using the MUMmer alignment. The red dots represent the synteny regions and the blue dots represent the rearrangement regions between the two strains. The lines connected by dots represent the high synteny regions. (B) Phylogenetic tree was constructed using hclust function in R package based on the average nucleotide identity (ANI) values of F. kyushuense WFK101 and other 7 strains of Fusarium. The whole genome sequences of 7 strains of Fusarium were obtained from GenBank and the ANI values were calculated using OrthoANI.

For this study, we used OrthoANI (Lee et al., 2016) to find the average ANI values between F. kyushuense WFK101 and 7 strains of FSSP (Laraba et al., 2021). The genome of F. kyushuense WFK101 showed about 83.85–98.80% identity with seven representative strains of FSSP. Even though they are only 83.85% alike, the chromosome structures of F. kyushuense WFK101 and F. asiaticum KCTC 16664 are very similar (Fig. 1A). ANI-based phylogenetic tree showed that the genome of F. kyushuense WFK101 had 98.80% identity with F. kyushuense NRRL (Fig. 1B).

Funannotate pipeline v.1.8.9 (Palmer and Stajich, 2020) was used to annotate genes, and the results of F. kyushuense WFK101 and F. kyushuense NRRL 25348 were compared (Table 1). Fusarium kyushuense WFK101 and F. kyushuense NRRL 25348 were found to have 47 secondary metabolite gene clusters using antiSMASH analyses (Blin et al., 2021). In the genomes of F. kyushuense WFK101 and F. kyushuense NRRL 25348, the trichothecene biosynthetic gene cluster was found on chromosome 2. The Tri16 gene, a key gene for type A trichothecene biosynthesis, was found next to the Tri1 gene on chromosome 1 (Wang et al., 2023). The complete genome sequence of F. kyushuense WFK101 can provide basic information about the synthesis of type A trichothecene of F. kyushuense.

Strain and nucleotide sequence accession number

Fusarium kyushuense WFK101 has been deposited in the Korean Collection for Type Cultures (KCTC) under the number KCTC 56956. The complete genome sequence of F. kyushuense WFK101 has been deposited in the NCBI GenBank database under the accession number JAWRWB000000000. The genome sequence of F. kyushuense WFK101 was also deposited at the National Agricultural Biotechnology Information Center (NABIC) under the accession number NG-1860- 000001–NG-1860-000018.

적 요

Fusarium kyushuense WFK101은 전라남도 보성의 논 주변에서 채집된 잡초, 들묵새에서 분리되었다. Fusarium kyushuense의 전장유전체는 Illumina HiSeq 2500 플랫폼을 사용하여 해독되었고 4개의 염색체가 확인되었다. Fusarium kyushuense WFK101와 Fusarium sambucinum species complex 내 대표 균주 간의 염기서열 평균 유사도 분석 결과, F. kyushuense NRRL 25348과 98.80%의 가장 높은 유사도를 보였다. 유전자 주석 분석 결과 F. kyushuense WFK101은 47개의 2차 대사산물 유전자 클러스터를 가지고 있으며, type A 트라이코세신 합성을 결정하는 Tri16 유전자는 1번 염색체 상의 Tri1 유전자 옆에 존재하는 것을 확인하였다. Fusarium kyushuense WFK101의 유전체 정보는 트라이코세신 중 가장 독성이 강한 type A 트라이코세신을 합성하는 F. kyushuense의 심층적인 유전정보를 제공한다.

Acknowledgments

This work was carried out with the support of “Cooperative Research Program for Agriculture Science and Technology Development (RS-2023-00230782)” Rural Development Administration, Republic of Korea, and the support of the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the Crop Viruses and Pests Response Industry Technology Development Program (Grant Number: 320036-5), which is funded by the Ministry of Agriculture.

Conflict of Interest

The authors declare that there is no conflict of interest.

References
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March 2024, 60 (1)
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  • Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)
      10.13039/501100014189
      320036-5