2014-06-05

Hybrid assembly of Talaromyces marneffei (ana. Penicillium marneffei) with Sanger, Illumina, PacBio RS reads

Standard RNA-seq of Talaromyces marneffei (ana. Penicillium marneffei) PM1 grown on PDA media under four experimental treatments: (1) stable growth at 37°C as yeasts, (2) yeasts grown at 37°C transferred to 25°C for 6 hours, (3) mycelia grown at 25°C transferred to 37°C for 6 hours, and (4) stable growth at 25°C as mycelia.

Systemic dimorphic fungi cause more than one million new infections each year, ranking them among the significant public health challenges currently encountered. Penicillium marneffei is a systemic dimorphic fungus endemic to Southeast Asia. The temperature-dependent dimorphic phase transition between mycelium and yeast is considered crucial for the pathogenicity and transmission of P. marneffei, but the underlying mechanisms are still poorly understood. Here, we re-sequenced P. marneffei strain PM1 using multiple sequencing platforms and assembled the genome using hybrid genome assembly. We determined gene expression levels using RNA sequencing at the mycelial and yeast phases of P. marneffei, as well as during phase transition. We classified 2,718 genes with variable expression across conditions into 14 distinct groups, each marked by a signature expression pattern implicated at a certain stage in the dimorphic life cycle. Genes with the same expression patterns tend to be clustered together on the genome, suggesting orchestrated regulations of the transcriptional activities of neighboring genes. Using qRT-PCR, we validated expression levels of all genes in one of clusters highly expressed during the yeast-to-mycelium transition. These included madsA, a gene encoding MADS-box transcription factor whose gene family is exclusively expanded in P. marneffei. Over-expression of madsA drove P. marneffei to undergo mycelial growth at 37°C, a condition that restricts the wild-type in the yeast phase. Furthermore, analyses of signature expression patterns suggested diverse roles of secreted proteins at different developmental stages and the potential importance of non-coding RNAs in mycelium-to-yeast transition. We also showed that RNA structural transition in response to temperature changes may be related to the control of thermal dimorphism. Together, our findings have revealed multiple molecular mechanisms that may underlie the dimorphic transition in P. marneffei, providing a powerful foundation for identifying molecular targets for mechanism-based interventions.

Yang, E, Chow, WN, Wang, G, Woo, PCY, Lau, SKP, Yuen, KY, Lin, X, Cai, JJ. (2014). Data from: Signature Gene Expression Reveals Novel Clues to the Molecular Mechanisms of Dimorphic Transition in Penicillium marneffei. [Data File]. The authors confirm that all data underlying the findings are fully available without restriction. Data are available in NCBI BioProject database under accession numbers: PRJNA251717 and PRJNA251718 at http://www.ncbi.nlm.nih.gov/bioproject/251717 and http://www.ncbi.nlm.nih.gov/bioproject/251718.
Click on “Linked Publications” to access the publication and access supporting information on figshare at https://figshare.com/articles/Signature_Gene_Expression_Reveals_Novel_Clues_to_the_Molecular_Mechanisms_of_Dimorphic_Transition_in_Penicillium_marneffei_/1206622

dimorphic fungi cause

genome

yeast

dimorphic life cycle

signature expression patterns

rna

gene expression levels

marneffei strain PM 1

signature expression pattern

transition

Penicillium marneffei

signature Gene Expression

phase