Jongbum Jeon, Ki-Tae Kim, Jaeyoung Choi, Kyeongchae Cheong, Jaeho Ko, Gobong Choi, Hyunjun Lee, Gir-Won Lee, Sook-Young Park, Seongbeom Kim, Sun Tae Kim, Cheol Woo Min, Seogchan Kang, Yong-Hwan Lee

RNA Biol.; 2022; 19(1):373-385.  doi: 10.1080/15476286.2022.2043040.

Abstract

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.

See https://pubmed.ncbi.nlm.nih.gov/35311472/

Fig. 1: Characteristics of AS in M. oryzae KJ201 under different conditions.

(a) Among 13,306 annotated genes of KJ201, 2,413 are subjected to AS under one or more conditions. Transcript isoforms from 29 and 499 genes were detected only in mycelia and during infection, respectively. The remaining 1,883 genes produced AS transcripts under both conditions. (b) The number of AS genes in each sample predicted using three FPKM values for cut-off. (c) PCA analysis of the annotated transcripts and their isoforms. The log2 FPKM values of individual transcripts within each sample are used to calculate PCA distances. The standard PCA function implemented in prcomp was used for this analysis.