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12:37
Pyrosequencing for Microbial Identification and Characterization
Published on: August 22, 2013
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches
Foo Cheung1, Joe Win, Jillian M Lang
1The J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850 USA. fcheung@jcvi.org
BMC Genomics
|November 19, 2008
Summary
This study generated a comprehensive set of transcribed sequences for the plant pathogen Pythium ultimum, revealing insights into its gene complement and identifying potential markers for genotyping and phylogenetic analysis.
Area of Science:
- Plant Pathology
- Genomics
- Molecular Biology
Background:
- Pythium species are significant agricultural plant pathogens.
- Understanding their molecular and genetic makeup is crucial.
- They are closely related to Phytophthora species and widely distributed.
Purpose of the Study:
- To characterize the gene complement of Pythium ultimum.
- To generate Expressed Sequence Tags (ESTs) for Pythium ultimum.
- To utilize both Sanger and pyrosequencing for transcriptome analysis.
Main Methods:
- Generated ESTs from Pythium ultimum using Sanger and pyrosequencing.
- Normalized cDNA libraries were used for high-throughput sequencing.
- Hybrid assembly of sequences from both methods was performed.
Main Results:
- Generated over 34,000 unique sequences through hybrid assembly.
- Identified sequences with similarity to known oomycete effectors and enzymes.
- Discovered novel sequences and 179 candidate simple sequence repeats for genotyping.
Conclusions:
- A robust set of transcribed sequences for Pythium ultimum was generated.
- Both Sanger and pyrosequencing were complementary, yielding unique sequences.
- The dataset provides resources for developing phylogenetic and diagnostic markers.
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