PacBio sequencing reveals transposable element as a key contributor to genomic plasticity and virulence variation in Magnaporthe oryzae.
The sustainable cultivation of rice, which serves as staple food crop for more than half of the world’s population, is under serious threat due to the huge yield losses inflicted by rice blast disease caused by the globally destructive fungus Magnaporthe oryzae (Pyricularia oryzae) (Dean et al., 2012, Nalley et al., 2016, Deng et al., 2017). This filamentous ascomycete fungus is also capable of causing blast infection on other economically important cereal crops, including wheat, millet, and barley, making it the world’s most important plant pathogenic fungus (Zhong et al., 2016). The advent of whole-genome sequencing technology and the subsequent deployment of next-generation sequencing (NGS) strategies have successfully generated genome assemblies for over 50 isolates of M. oryzae, which have played an instrumental role in enhancing our understanding of how rice blast fungus undertakes host adaptation, host specificity, and host range expansion to overcome host resistance (Dean et al., 2005, Xue et al., 2012, Wu et al., 2015, Zhang et al., 2016). However, research findings obtained from comparative genomic studies conducted using the NGS-assembled genome do not present an in-depth account of the genomic features that contribute to the prevailing genomic variations among M. oryzae species, because NGS assemblies are highly fragmented and lack most of the lineage-specific (LS) regions, which are more plastic than the core genome and enriched with repeats and effector proteins (Raffaele and Kamoun, 2012, Faino et al., 2016).