title: Exploring structural variants in environmentally sensitive gene families.
abstract: Environmentally sensitive plant gene families like NBS-LRRs, receptor kinases, defensins and others, are known to be highly variable. However, most existing strategies for discovering and describing structural variation in complex gene families provide incomplete and imperfect results. The move to de novo genome assemblies for multiple accessions or individuals within a species is enabling more comprehensive and accurate insights about gene family variation. Earlier array-based genome hybridization and sequence-based read mapping methods were limited by their reliance on a reference genome and by misplacement of paralogous sequences. Variant discovery based on de novo genome assemblies overcome the problems arising from a reference genome and reduce sequence misplacement. As de novo genome sequencing moves to the use of longer reads, artifacts will be minimized, intact tandem gene clusters will be constructed accurately, and insights into rapid evolution will become feasible.
authors: Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108, USA; Department of Plant Biology, 220 BioScience Building, University of Minnesota, St. Paul, MN 55108, USA. Electronic address: neviny@umn.edu.
authors: Nevin Dale
authors: ND
authors: Young
authors: Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108, USA; Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA.
authors: Peng
authors: P
authors: Zhou
authors: Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA.
authors: Kevin At
authors: KA
authors: Silverstein
mesh_terms: D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods; D010940:Plant Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins