Genome Sequence Resource of Fusarium brachygibbosum Padwick Strain HN-1, a Causal Agent of Maize Stalk Rot Disease
- Hafiz Abdul Haseeb1 2
- Sajjad Hyder3
- Meixu Gao1
- Wei Guo1 †
- 1Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
- 2Directorate General of Pest Warning and Quality Control of Pesticides, Punjab, Lahore, Pakistan
- 3Department of Botany, Government College Women University, Sialkot, Pakistan
Fusarium brachygibbosum Padwick, the causal agent of stalk rot disease, is a threat to the maize crop in China. However, genomic information of the pathogen is not available yet. The current study presented the genomic information of F. brachygibbosum, isolated from maize. The genome size is 40.36 Mb and consists of 12,510 genes. The GC content is 47.95%, and there are 913 predicted secretory proteins. The presented genomic data highlighted the virulence features, plant–microbe interaction ability, genes associated with the pathogen’s metabolic processes, and host-binding ability. Presented results would extend our knowledge of the pathogen and help us develop suitable disease management strategies.
Fusarium spp. are notorious worldwide pathogens causing various plant diseases and possess a broad host range, including wheat, maize, soybean, sunflower, sugar beet, date palms, desert squash, oleander, almond, and so on. (Ali et al. 2020; Al-Mahmooli et al. 2013; Al-Sadi et al. 2012; Cao et al. 2018; Mirhosseini et al. 2014; Shan et al. 2017; Stack et al. 2017; Wang et al. 2021; Xia et al. 2018). Based on the DNA features, about 23 species complexes are reported in the Fusarium genus (Jacobs-Venter et al. 2018). Fusarium stalk rot of maize has been reported throughout the global maize-growing regions. Previously, we have reported Fusarium brachygibbosum Padwick strain HN-1 as a causal agent of stalk rot disease of maize in China (Shan et al. 2017). However, the whole-genome sequence has not been reported yet. With the availability of the whole-genome sequence, understanding of the pathogen will be improved, and suitable management strategies will be developed to control disease caused by the pathogen.
Genomic DNA was purified from the mycelium of F. brachygibbosum Padwick strain HN-1 using a commercial DNA extraction kit (DNASecure Plant Kit; TianGen) following the manufacturer’s instructions. The integrity of harvested DNA was detected by agarose gel electrophoresis and quantified by Qubit (version 2.0). Whole-genome sequencing was performed on the Illumina HiSeq 2500-PE125 platform with massively paralleled sequencing technology by following the standard procedures (5-kb mate-pair library and 500-bp A-tailed pair-end Illumina library). The genome was sequenced by the Beijing Novogene Bioinformatics Technology Co., Ltd., Beijing, China (https://en.novogene.com). The paired reads were filtered using the compiling pipeline provided by the company. After quality control, the reads were assembled using the SOAPdenovo program (version 2.04) (Li et al. 2008, 2010). Related coding genes were retrieved using the Augustus program (version 2.7) (Stanke et al. 2008). The RepeatMasker program (version open-4.0.5) was used to predict the interspersed repetitive sequences (Saha et al. 2008), whereas tandem repeats were analyzed in Tandem Repeats Finder (version 4.07b) (Benson 1999). Transfer RNA (tRNA)- and ribosomal RNA (rRNA)-related genes were predicted by tRNAscan-SE and rRNAmmer programs, respectively (Lagesen et al. 2007; Lowe and Eddy 1997). Small nuclear RNAs was predicted through a BLAST search in the Rfam database using the Cmsearch program with default parameters (Gardner et al. 2009; Nawrocki et al. 2009). A whole-genome Blastp (Altschul 1997) search (E-value < 1e-5, minimal alignment length percentage > 40%) was performed against seven databases, including the Nonredundant Protein (NR) (Saier et al. 2016), gene ontology (GO) (Ashburner et al. 2000), Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa 2006), clusters of orthologous groups (COG V9.05) (Galperin et al. 2015), Transporter Classification Database (TCDB) (Saier et al. 2016), Swiss-Prot., and TrEMBL databases (Boeckmann 2003). Secretory proteins were analyzed using Signal P (5.0) (Almagro Armenteros et al. 2019) and TMHMM (Krogh et al. 2001), whereas genes potentially involved in the pathogen–host interactions were searched in the pathogen–host interaction (PHI) database (Urban et al. 2017). For carbohydrate-active enzymes (CAZymes) prediction, related genes were searched in the CAZy database using dbCAN (Yin et al. 2012).
The assembly of the F. brachygibbosum genome was 40.36 Mb (100× coverage) in size, which consists of 12,510 coding genes having GC content of 47.95%. The genome comprises 277 scaffolds with a total scaffold length of 40,359,238 bp and N50 length of 3,082,799 bp. The maximum scaffold length was 5,093,487 bp, while the minimum scaffold length was 504 bp. In all, 11,998 genes were predicted with the average gene length of 1,387 bp using the Augustus program. For functional annotations, 11,998, 3,870, 2,189, 7,684, and 488 genes were annotated from NR, KEGG, COG, GO, and TCDB databases, respectively. In total, 913 putative secretory proteins were identified in the genome using Signal P and TMHMM. dbCAN predicted a total of 511 genes from the CAZymes, including 250 genes related to glycoside hydrolases, 80 to glycosyl transferases, 19 related to polysaccharide lyases, 31 related to carbohydrate esterases, 71 predicted to have auxiliary activities, and 60 genes associated with carbohydrate-binding modules. Similarly, it was predicted that 1,285 genes from F. brachygibbosum HN-1 were PHI genes. The genome assembly statistics are shown in Table 1.
The complete genomic data have been deposited to the NCBI GenBank database under the accession number JAEKIX000000000. The genome’s contig information can be assessed at NCBI under the BioProject ID PRJNA686892 and BioSample ID SAMN17127420. The version described in this article is JAEKIX000000000.1. The presented genomic information of F. brachygibbosum will provide a base for the researchers to design an effective control strategy against the pathogen.
We thank H. Kang at the Institute of Plant Protection, Chinese Academy of Agricultural Sciences for his consistent support for our genome projects.
The author(s) declare no conflict of interest.
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Funding: This research work was partially supported by the National Key Research and Development Program of China (grant number 2017YFC1600903) and National Natural Science Foundation of China (grant numbers 31670143 and 32072377).
The author(s) declare no conflict of interest.