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New M. Oryzae Assembly Reveals Importance of Previously Missed Transposable Elements

Thursday, April 5, 2018

Rice pathogen genome assembly

Rice blast symptoms. Photo by Donald Groth.

A publication from the Molecular Plant journal demonstrates the use of SMRT Sequencing to characterize activity of transposable elements in Magnaporthe oryzae, the destructive fungus responsible for rice blast disease. This information will help scientists better understand pathogen biology and potentially find new ways to reduce its impact on an important food source.

Lead authors Jiandong Bao, Meilian Chen, Zhenhui Zhong, Wei Tang, senior author Zonghua Wang, and collaborators at Fujian Agriculture and Forestry University and Minjiang University report their findings in “PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae.”

They embarked on the study because “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 the huge yield losses inflicted by the rice blast disease,” they write. Until this project, however, some 50 previous short-read genome assemblies were not of sufficient quality to support the kinds of in-depth investigations required to understand the pathogen’s genetic mechanisms or variation across species. These 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,” the scientists explain.

To build a better assembly, the team applied PacBio long-read sequencing to the challenge. They produced high-quality, nearly complete genome representations for two M. oryzae isolates. The resulting assemblies were far more contiguous than previous ones, with contig N50s increased to 3.28 Mb and 4.13 Mb, compared to 180 kb and 156 kb respectively for short-read assemblies. That led to a “>95% reduction in genome fragmentation,” the scientists report, and “approximately 98% of the PacBio assembled contigs were longer than 100 kb.” Alignment to the reference genome filled about 70% of sequence gaps and “confirmed that PacBio assemblies have sufficient genome coverage and superior integrity,” the team adds.

Importantly, the PacBio assemblies were about 10% larger than the short-read assemblies. Analysis of this “showed that the increased size of PacBio assembled genome was not accompanied by a corresponding increase in the number of new genes, but was as a result of significant increase in the recovery of repeat sequence,” the scientists write. That new content included many transposable elements, with some entirely novel elements detected. The scientists also analyzed the effects of transposable elements and determined that they “play a key role in regulating genomic plasticity, promote chromosome rearrangement and presence/absence polymorphism of [secreted protein] genes,” the team writes.

This study offers strong validation of the importance of transposable elements in pathogen virulence and demonstrates the utility of SMRT Sequencing for achieving high-quality assemblies to fully represent these elements.

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