Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

Authors: XIONG, DIANGUANG - Beijing Forestry University; WANG, YONGLIN - Beijing Forestry University; MA, JIE - Beijing Forestry University; Klosterman, Steven; XIAO, SHUXIAO - Beijing Forestry University; TIAN, CHENGMING - Beijing Forestry University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2014
Publication Date: 5/1/2014
Citation: Xiong, D., Wang, Y., Ma, J., Klosterman, S.J., Xiao, S., Tian, C. 2014. Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae. BMC Genomics. 15:324.

Interpretive Summary: Verticillium dahliae is a soil-borne plant pathogenic fungus that penetrates roots, colonizes the water conducting xylem vessels, leading to symptoms of vascular wilt. The fungus is capable of surviving for years in the soil, even in the absence of a plant. The fungus produces long-lived pigmented structures known as microsclerotia, which are resistant to degradation in the soil. To gain insight into genes of this pathogen that are important for the formation of microsclerotia, and hence survival of the pathogen in soil, comprehensive gene expression analyses were conducted at several stages of microsclerotial development. These analyses revealed hundreds of fungal genes that are differentially expressed among the different developmental stages examined, suggesting the importance of these genes in microsclerotial development. This study sheds light on potential targets for further examination in functional studies and may provide insight into alternative control measures, based upon the gene products identified.

Technical Abstract: Verticillium dahliae is a soil-borne fungus that causes vascular wilt diseases in a wide range of plant hosts. V. dahliae produces multicelled, melanized resting bodies, also known as microsclerotia (MS) that can survive for years in the soil. Thus, MS formation marks an important event in the disease cycle of V. dahliae. In this study, next generation sequencing technology of RNA-Seq was employed to investigate the global transcriptomic dynamics of MS development to identify differential gene expression at several stages of MS formation. We observed large-scale changes in gene expression during MS formation, such as increased expression of genes involved in protein metabolism and carbohydrate metabolism. Cluster analyses revealed increased expression of genes encoding products involved in primary metabolism and stress responses throughout MS development. Signaling pathway-associated genes in a separate cluster showed increased expression early in MS formation, followed by decreased levels at the later stages. Homologs of genes located in the lineage-specific (LS) regions of strain VdLs.17, some of which have been ascribed to virulence functions, were either not expressed or showed low expression, suggesting that genes present in LS regions do not contribute to MS formation. Furthermore, we identified 2,780 novel transcription regions and two novel genes were discovered and annotated. Alternative splicing events were analyzed, revealing that over 95% AS events involve intron retention. These data reveal the dynamics of transcriptional regulation during MS formation and were used to construct a comprehensive high-resolution gene expression map. This map provides a key resource for understanding the biology and molecular basis of MS development of V. dahliae.