Genome Sequence Analysis of the Fungal Pathogen Fusarium graminearum Using Oxford Nanopore Technology.

Zhigang Hao,Jiaqing Xu,Yuanyuan Li,Jianqiang Li,Laixin Luo,Yunyun Jiang

doi:10.3390/jof7090699

Zhigang Hao, Jiaqing Xu + Show 4 more

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https://doi.org/10.3390/jof7090699

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Abstract

Fusarium graminearum is a plant pathogen of global importance which causes not only significant yield loss but also crop spoilage due to mycotoxins that render grain unsafe for human or livestock consumption. Although the full genome of several F. graminearum isolates from different parts of the world have been sequenced, there are no similar studies of isolates originating from China. The current study sought to address this by sequencing the F. graminearum isolate FG-12, which was isolated from the roots of maize seedlings exhibiting typical symptoms of blight growing in the Gansu province, China, using Oxford Nanopore Technology (ONT). The FG-12 isolate was found to have a 35.9 Mb genome comprised of five scaffolds corresponding to the four chromosomes and mitochondrial DNA of the F. graminearum type strain, PH-1. The genome was found to contain an approximately 2.23% repetitive sequence and encode 12,470 predicted genes. Additional bioinformatic analysis identified 437 genes that were predicted to be secreted effectors, one of which was confirmed to trigger a hypersensitive responses (HR) in the leaves of Nicotiana benthamiana during transient expression experiments utilizing agro-infiltration. The F. graminearum FG-12 genome sequence and annotation data produced in the current study provide an extremely useful resource for both intra- and inter-species comparative analyses as well as for gene functional studies, and could greatly advance our understanding of this important plant pathogen.

Highlights

Fusarium graminearum is a plant pathogen of global significance which causes dramatic yield loss and reduces grain quality via the production of mycotoxins harmful to both humans and animals [1]
The FG-12 genome exhibited a high degree of homology with the F. graminearum type strain PH-1, there were some key differences
The Chinese FG-12 isolate was found to lack a small region located at the carboxyl terminus of chromosome 4 in the PH-1 genome. This region was found to encode 83 putative genes, many of which were ascribed to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with thermogenesis, which is a pathway known to be associated with environmental adaptation [31,32]

Summary

Introduction

Fusarium graminearum is a plant pathogen of global significance which causes dramatic yield loss and reduces grain quality via the production of mycotoxins harmful to both humans and animals [1] This ascomycete fungus infects many cereal crops, including rice and oats, and is responsible for Fusarium head blight (FHB) in wheat and barley as well as Fusarium ear blight (FEB) and stem rot in maize. These diseases pose a serious threat to global food production [2]. It is critical to gain a better understanding of the F. graminearum–host interaction in order to develop more effective methods of control

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