Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV)

Abstract

Recently, a novel poplar mosaic disease caused by bean common mosaic virus (BCMV) was investigated in Populus alba var. pyramidalis in China. Symptom characteristics, physiological performance of the host, histopathology, genome sequences and vectors, and gene regulation at the transcriptional and posttranscriptional levels were analyzed and RT−qPCR (quantitative reverse transcription PCR) validation of expression was performed in our experiments. In this work, the mechanisms by which the BCMV pathogen impacts physiological performance and the molecular mechanisms of the poplar response to viral infection were reported. The results showed that BCMV infection decreased the chlorophyll content, inhibited the net photosynthesis rate (Pn) and stomatal conductance (Gs), and significantly changed chlorophyll fluorescence parameters in diseased leaves. Transcriptome analysis revealed that the expression of the majority of DEGs (differentially expressed genes) involved in the flavonoid biosynthesis pathway was promoted, but the expression of all or almost all DEGs associated with photosynthesis-antenna proteins and the photosynthesis pathway was inhibited in poplar leaves, suggesting that BCMV infection increased the accumulation of flavonoids but decreased photosynthesis in hosts. Gene set enrichment analysis (GSEA) illustrated that viral infection promoted the expression of genes involved in the defense response or plant-pathogen interaction. MicroRNA-seq analysis illustrated that 10 miRNA families were upregulated while 6 families were downregulated in diseased poplar leaves; moreover, miR156, the largest family with the most miRNA members and target genes, was only differentially upregulated in long-period disease (LD) poplar leaves. Integrated transcriptome and miRNA-seq analyses revealed 29 and 145 candidate miRNA−target gene pairs; however, only 17 and 76 pairs, accounting for 2.2% and 3.2% of all DEGs, were authentically negatively regulated in short-period disease (SD) and LD leaves, respectively. Interestingly, 4 miR156/SPL (squamosa promoter-binding-like protein) miRNA−target gene pairs were identified in LD leaves: the miR156 molecules were upregulated, but SPL genes were downregulated. In conclusion, BCMV infection significantly changed transcriptional and posttranscriptional gene expression in poplar leaves, inhibited photosynthesis, increased the accumulation of flavonoids, induced systematic mosaic symptoms, and decreased physiological performance in diseased poplar leaves. This study elucidated the fine-tuned regulation of poplar gene expression by BCMV; moreover, the results also suggested that miR156/SPL modules played important roles in the virus response and development of viral systematic symptoms in plant virus disease.

Why the adventitious roots of poplar are so colorful: RNAseq and metabolomic analysis reveal flavonols, flavones, and anthocyanins accumulation in canker pathogens-induced adventitious roots in poplar

“…were also significantly upregulated (Liu et al 2022b), suggesting a de novo biosynthesis of flavonoids and anthocyanins in duckweed variety. In our recent study, aside from gene FLS, gene PAL, CHS, CHI, F3H, DFR, ANS, LAR, and ANR are all upregulated, suggesting a de novo biosynthesis of flavonoids in the BCMV (bean common mosaic virus) infected poplar leaves (Wang et al 2023). However, one recent research illustrated that ANS genes negatively but BZ1 genes positively regulate the biosynthesis of anthocyanins in poplar 84K leaves (Yan et al 2022).…”

“…Because some SPLs also are the targets of miR156, then this microRNA can positively control the level of flavonoids/anthocyanins in citrus and switchgrass (Cai et al 2022; Feng et al 2022) and poplar (Wang et al 2020b). Our recent research also illustrated that miR156-SPL modules are involved in the biosynthesis of flavonoids or the development of mosaic symptoms in poplar-BCMV interaction (Wang et al 2023). Specifically, the expression of miR156 and a series of flavonoid/anthocyanin biosynthesis-related genes (including PAL, CHS, CHI, F3H, DFR, ANS, LAR, and ANR) were upregulated and the expression of four SPL genes (such as gene PAYG024925) were downregulated, however, none R2R3-MYB gene or “MBW” complex significant changed in the poplar mosaic leaves (Wang et al 2023).…”

“…Our recent research also illustrated that miR156-SPL modules are involved in the biosynthesis of flavonoids or the development of mosaic symptoms in poplar-BCMV interaction (Wang et al 2023). Specifically, the expression of miR156 and a series of flavonoid/anthocyanin biosynthesis-related genes (including PAL, CHS, CHI, F3H, DFR, ANS, LAR, and ANR) were upregulated and the expression of four SPL genes (such as gene PAYG024925) were downregulated, however, none R2R3-MYB gene or “MBW” complex significant changed in the poplar mosaic leaves (Wang et al 2023). Interestingly, the same SPL gene (PAYG024925), which was identified in poplar mosaic leaves, was also downregulated in the present poplar ARs (Supplementary file 9), suggesting sunlight exposure increasing the accumulation of flavonoids metabolites at the post-transcriptional level, through miR156-SPL module which increases the stability of “MBW” complex.…”

Molecular Characterization of an Isolate of Bean Common Mosaic Virus First Identified in Gardenia Using Metatranscriptome and Small RNA Sequencing

“…With the extensive investigation of plant viruses and the widespread use of high-throughput sequencing technology, more and more hosts outside the leguminous plants have been found to be natural hosts of BCMV. According to the published literature, there are currently at least four plant species outside the family Leguminosae found to be the natural host of BCMV, including Cudrania tricuspidata ( Seo et al, 2015 ), Alpinia purpurata ( Larrea-Sarmiento et al, 2020 ), Nandina domestica ( Su et al, 2022 ), and Populus alba ( Wang et al, 2023 ). Among them, only BCMV identified in Cudrania tricuspidata and Nandina domestica are reported with complete genome sequence.…”

“…In contrast to some potyviruses like soybean mosaic virus (SMV), which exhibits a narrow host range limited to a few plants ( Hajimorad et al, 2018 ), BCMV exhibits an extensive host range, infecting over 100 plants across 44 genera. Nevertheless, the hosts of BCMV are generally thought to be restricted to leguminous plants ( Sáiz et al, 1994 ; Wang et al, 2023 ). With the rapid development of high-throughput sequencing technology, more and more plants outside legume species have been reported as novel hosts of BCMV, including Cudrania tricuspidata ( Seo et al, 2015 ), Alpinia purpurata ( Larrea-Sarmiento et al, 2020 ), and Nandina domestica ( Su et al, 2022 ).…”