Discovery of new soybean and soybean rust genes using next generation sequencing

Authors: Tremblay, Arianne; HOSSEINI, PARSA - Towson University; Li, Shuxian; ALKHAROUF, NADIM - Towson University; Matthews, Benjamin - Ben

Submitted to: American Phytopathology Society
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2011
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Soybean is one of the top five agricultural products in the United States and is highly susceptible to soybean rust (SR), an exotic obligate fungus that arrived in the USA in 2004. We used mRNA-Seq by Illumina/Solexa to analyze gene expression patterns of the host and pathogen at different time points during infection of the leaf. Over 6 million sequences were obtained for each time-point. DNA sequences were aligned to the soybean genome and to SR EST sequences. Tag counts were obtained for each gene and used as a measure of expression of each gene. Then expression levels in infected leaf cells were compared to the uninfected control. Expression levels of genes encoding enzymes were overlaid on biochemical pathway diagrams from the Kyoto Encylcopedia of Genes and Genomes to visualize changes. New generation sequencing allows discovery of new genes. We found sequences aligning to portions of the soybean genome with no gene annotation. A good example of this is a contig built from 699 sequence tags aligning to chromosome 6, between base pair 48,935,656 and 48,935,919. This sequence of 263 base pairs resides within a long stretch of 14,628 base pairs on chromosome 6 where no gene has been annotated. Translation of this stretch of nucleotides revealed one open reading frame with a potential to encode five short proteins ranging from 70 to 179 amino acids. The first four proteins had high similarity to retrotransposon protein from soybean and rice while the last protein had high similarity to a disease resistance protein from Brassica rapa. Many other contigs did not align to the soybean genome and did not have homology to SR sequences. Sequence information on SR is limited, therefore many of these unknown sequences may be SR sequences. Some of the contigs not matching current soybean and SR databases had similarity with genes in the NCBI database including genes involved in fungal development, lignin degradation, signal transduction and intracellular communication (chitin deacetylase, glyoxal oxidase, serine threonine protein phosphatase, transthyretin). However, most of the contigs did not shared similarity with genes in NCBI database but a manual homology search against different domain databases gave us numerous contigs encoding proteins containing signal peptides which are common to fungal virulence factors. We also found contigs encoding proteins containing catalase and peroxidase domains, which are involved in defense. Such information may be use to update our knowledge of the soybean and SR genomes and to develop new methods to broaden resistance of soybean to soybean rust.