SCNBase: A Community Resource for Soybean Cyst Nematode (Heterodera glycines) Genomics

Soybean cyst nematode (SCN) is the most damaging pathogen to soybean productivity in North America. Currently annual yield losses are estimated at $1.2 billion. Though SCN-resistant soybean varieties are available, constant rotation is necessary to avoid the development of resistance in quick-adapting and persistent SCN populations. We are developing a community driven web resource called SCNBase using GMOD tools to visualize the SCN genome, transcriptome, and molecular data. To generate a long-lasting, and community-friendly website we are using a Tripal/Drupal platform that generates forms to simplify content creation and data curation.

As a first step, we assembled a draft genome using PacBio long-read sequencing technology, overcoming assembly challenges from high levels of heterozygosity and repeat content. The assembly contains approximately 20,064 genes in 738 scaffolds with 124.5 Mb nucleotide content, 33.6% of which are repetitive. In SCNBase, we will utilize comparative genomics to further understand nematode adaptation and evolution. Thus far, syntenic blocks have only been discovered between closely related clades, which has been useful for improving the SCN genome assembly and annotation. We intend for this resource to give insight into the essentiality or expendability of genes during the evolution of obligate parasitism in nematodes, thus giving the SCN community the resources to design better pest management practices.