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Open Access Research article

Analysis of Phakopsora pachyrhizi transcript abundance in critical pathways at four time-points during infection of a susceptible soybean cultivar using deep sequencing

Arianne Tremblay16*, Parsa Hosseini23, Shuxian Li4, Nadim W Alkharouf5 and Benjamin F Matthews1

Author Affiliations

1 Soybean Genomics & Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA

2 Bioinformatics/Computational Biology, George Mason University, 4400 University Dr. Manassas, Fairfax, VA 22030, USA

3 Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA

4 USDA-ARS, Crop Genetics Research Unit, Stoneville, MS 38776, USA

5 Molecular Biology, Biochemistry and Bioinformatics, Fischer College of Science and Mathematics, Towson University, 8000 York Road, Towson, MD 21252, USA

6 Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, BS411/412, Baltimore, MD 21250, USA

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BMC Genomics 2013, 14:614  doi:10.1186/1471-2164-14-614

Published: 11 September 2013



Phakopsora pachyrhizi, the causal agent responsible for soybean rust, is among the top hundred most virulent plant pathogens and can cause soybean yield losses of up to 80% when appropriate conditions are met. We used mRNA-Seq by Illumina to analyze pathogen transcript abundance at 15 seconds (s), 7 hours (h), 48 h, and 10 days (d) after inoculation (ai) of susceptible soybean leaves with P. pachyrhizi to gain new insights into transcript abundance in soybean and the pathogen at specific time-points during the infection including the uredinial stage.


Over three million five hundred thousand sequences were obtained for each time-point. Energy, nucleotide metabolism, and protein synthesis are major priorities for the fungus during infection and development as indicated by our transcript abundance studies. At all time-points, energy production is a necessity for P. pachyrhizi, as indicated by expression of many transcripts encoding enzymes involved in oxidative phosphorylation and carbohydrate metabolism (glycolysis, glyoxylate and dicarboxylate, pentose phosphate, pyruvate). However, at 15 sai, transcripts encoding enzymes involved in ATP production were highly abundant in order to provide enough energy for the spore to germinate, as observed by the expression of many transcripts encoding proteins involved in electron transport. At this early time-point, transcripts encoding proteins involved in RNA synthesis were also highly abundant, more so than transcripts encoding genes involved in DNA and protein synthesis. At 7 hai, shortly after germination during tube elongation and penetration, transcripts encoding enzymes involved in deoxyribonucleotide and DNA synthesis were highly abundant. At 48 hai, transcripts encoding enzymes involved in amino acid metabolism were highly abundant to provide for increased protein synthesis during haustoria maturation. During sporulation at 10 dai, the fungus still required carbohydrate metabolism, but there also was increased expression of transcripts encoding enzymes involved in fatty acid metabolism.


This information provides insight into molecular events and their timing throughout the life cycle of the P. pachyrhizi, and it may be useful in the development of new methods of broadening resistance of soybean to soybean rust.

Deep sequencing; Transcript abundance; Phakopsora pachyrhizi; Plant-pathogen interaction; Soybean; Soybean rust