gsrc: an R package for genome structure rearrangement calling.

Abstract

Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset. The compiled R-package and source code are available at http://cran.r-project.org/web/packages/gsrc/ . birgit.samans@uni-giessen.de. Supplementary data are available at Bioinformatics online.