Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.)

Abstract

Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

“…In the Oryza genus, the O. japonica genome had more fusion genes compared to O. indica, O. barthii and O. glaberrima (Zhou et al, 2022b) whereas differential gene fusions were observed among different Papaver species affecting alkaloid concentration (Catania et al, 2022). However, the gene fusions reported in sesame, particularly in Swetha are much higher than in maize (Zhou et al, 2022a) and Oryza (Zhou et al, 2022b). The duplication of parental genes prior to fusion was evident also in the sesame genome (Zhou et al, 2022b) while most of the added domains were products of horizontal transfer.…”

“…In higher plant genomes gene fusion is a complex process with a poorly understood evolutionary mechanism. Gene fusion events have been reported in the biosynthesis of alkaloids in opium poppy (Catania et al, 2022), viral infection in maize (Zhou et al, 2022a) and in the evolution of new genes in the genus Oryza (Zhou et al, 2022b). In the sesame pan-genome, 2.3% of AP2/ERF genes and 10% of WRKY genes were products of gene fusion.…”

Eukaryotic splicing machinery in the plant–virus battleground

“…In another study, changes in AS substantially identified sugarcane mosaic virus‐induced proteomic changes in sugarcane (Du et al, 2020). Furthermore, AS‐mediated transcriptional regulation is essential in resistance to RBSDV infection in maize (Zhou et al, 2022).…”

“…Genome‐wide variable splicing dynamics occur during plant virus infection, filling a knowledge gap (Mandadi & Scholthof, 2015). To date, AS has been studied to a lesser extent in plant virus diseases, such as MRDV caused by RBSDV (Zhou et al, 2022).…”

“…Plant virus disease is caused by plant virus parasitism. To date, some involvement of AS in the regulation of plant viruses has been reported (Table 1), including viruses infecting dicotyledonous plants, such as cauliflower mosaic virus (CaMV; Bouton et al, 2015), citrus chlorotic virus (Ma et al, 2015), beet curly top Iran virus (BCTIV; Bozorgi et al, 2017), and those infecting monocotyledon plants, such as maize streak virus (MSV; Wright et al, 1997), wheat dwarf virus (WDV; Gao et al, 2004), and rice black-streaked dwarf virus (RBSDV; Zhou et al, 2022; Figure 1), among others. Wild plant domestication for agriculture has impacted evolutionary changes in the virus.…”