Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple
mRNA and
protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS
isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host
infection stages. We identified 4,270 AS
isoforms derived from 2,413 genes, including 499 genes presumably regulated by
infection-specific AS. AS appears to increase during
infection, with 32.7% of the AS
isoforms being produced during
infection but absent in mycelia. Analysis of the
isoforms observed at each
infection stage showed that 636 AS
isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant
isoforms were predicted to encode regulatory
proteins such as
transcription factors and phospho-
transferases. We also identified the genes encoding distinct
proteins via AS and confirmed the translation of some
isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during
infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice
infection.