Characterization of the Two-Speed Subgenomes of Fusarium graminearum Reveals the Fast-Speed Subgenome Specialized for Adaption and Infection.

Qinhu Wang,Huiquan Liu,Changjun Chen,Chenfang Wang,Jin-Rong Xu,Cong Jiang

doi:10.3389/fpls.2017.00140

Abstract

Fusarium head blight, caused by Fusarium graminearum, is one of the most severe diseases on wheat and barley worldwide. Although the genomic data of several strains were published, the intragenomic variation of F. graminearum was not well characterized. Here, we sequenced three Chinese strains and conducted genome-wide comparisons. Our data revealed that all the sequenced strains were distinct from each other and over 350 genes were functionally lost in each of them. Variants of each strain were unevenly distributed in a highly conserved pattern along the chromosomes, resulting in a conserved two-speed genome. The fast subgenome has a lower GC content, shorter gene length, and higher variation of exon numbers than the slow subgenome. Genes related to interaction and pathogenicity, under positive selection, and up-regulated in planta were all significantly enriched in the fast subgenome. Furthermore, we found that the fast subgenome coincided with facultative heterochromatin regions that were repressed in vegetative stage but activated during infection as measured by RNA-seq and ChIP-seq data, suggesting that the fast subgenome is epigenetically regulated. Taken together, our data demonstrated that F. graminearum has a highly conserved two-speed genome and the fast subgenome responsible for adaption and infection is under the control of heterochromatin.

Highlights

IntroductionFusarium head blight (FHB), caused by Fusarium graminearum, is a great threat to the yields and quality of wheat, barley, and maize that directly relates to the survival and heath of human beings (Goswami and Kistler, 2004)
Wheat is one of the most cultivated staple crops that feed the world
Intraspecies comparison of an American strain GZ3639, which was shotgun sequenced with only 0.4-fold coverage, with the PH1 revealed that the high single-nucleotide polymorphism (SNP) regions were correlated with pathogen specialization and mainly located in the telomeric or sub-telomeric regions (Cuomo et al, 2007)

Summary

Introduction

Fusarium head blight (FHB), caused by Fusarium graminearum, is a great threat to the yields and quality of wheat, barley, and maize that directly relates to the survival and heath of human beings (Goswami and Kistler, 2004). The FHB outbreak in 2012 is extremely destructive and over one-third of the wheat growing areas were affected (Mehta, 2014). The whole genome sequencing of F. graminearum American strain PH-1 revealed that the pathogen has very few repeats sequences and much more transcription factors and hydrolytic enzymes than other fungi (Cuomo et al, 2007). Intraspecies comparison of an American strain GZ3639, which was shotgun sequenced with only 0.4-fold coverage, with the PH1 revealed that the high single-nucleotide polymorphism (SNP) regions were correlated with pathogen specialization and mainly located in the telomeric or sub-telomeric regions (Cuomo et al, 2007). Further studies showed that the Fusarium pathogens have the bipartite (two-speed) genome architecture (Zhao et al, 2014; Sperschneider et al, 2015) as what happened in many other pathogens (Dong et al, 2015), such as oomycete pathogen Phytophthora infestans (Haas et al, 2009) and fungal pathogen Leptosphaeria maculans (Dong et al, 2015)

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Conclusion