Xiaoqiu Huang has developed a number of computer programs for analysis of DNA and protein sequences. In 2003, he finalized the first version of PCAP (Parallel Contig Assembly Program), through funding from the National Human Genome Research Institute. He continues to improve the program as new sequencing equipment is developed and released. PCAP has proven to be a top genome sequence assembly program that has decoded genomes from fruit flies, worms, chimps, chicken, and several types of fungi. This year, Huang is participating on a multi-pronged research effort through a USDA $1.7M grant with an end goal to develop a genetically modified soybean variety that is resistant to sudden death syndrome. Huang's role is to use his PCAP program to decode the genetic sequence of Fusarium virguliforme, the fungal pathogen that causes sudden death syndrome in soybean plants.
Sudden death syndrome appeared in soybean fields in the early 1970s in Arkansas. In a few short decades, it has spread across the states, devastating fields and resulting in millions of dollars in crop losses. National crop losses in 2010, a particularly bad year for sudden death syndrome, totaled up to $1 billion. Even modern varieties of the plant are susceptible to the disease. The research team, led by Madan Bhattacharyya, Associate Professor of Agronomy at ISU, discovered a single protein produced by the fungus in the roots of the soybean plant that causes sudden death syndrome.
Huang produced the first genome sequence on the fungus from short sequences generated by the research team in 2010, to establish a baseline for later comparison. For the current project, 150 isolates (samples) from Iowa, and other parts of North and South America, were collected, and their sequences analyzed. DNA samples are too small to read directly, so in order to identify the full genome, Huang works with short sequences, running PCAP to identify overlaps to create the full genome. Short sequences are 500-800 nucleotides long. The fungus full genome sequence is 50 million nucleotides. "Sequencing genomes can involve huge amounts of data. In a chimpanzee, there are 40 million short sequences that translate to more than 30 gigabytes of data. It is too much for one CPU to handle, which is why PCAP is effective. It divides the computation into parallel processes," says Huang.
"The genome of the fungus causing sudden death in soybean plants mutates quickly, so we expect research results from our work," says Huang. "The genomes of isolates of this fungus are different depending on the geographical region in which they are found. This itself is interesting, and contradicts modern scientific thought because this fungus only has one genome type, propagated asexually. There should be no mutation. Our work indicates that there is a mechanism that induces mutation, indicating the possibility that cloning is not an evolutionary dead end."
Dr. Huang's work is funded by the National Institute of Food and Agriculture/USDA grant "Transgenic Approaches in Managing Sudden Death Syndrome in Soybean," 2013.
Huang's previous work on sequencing the Fusarium virguliformae genome was funded by the Soybean Research and Development Council, 2009-10.