Tracking the ancestry of known and 'ghost' homeologous subgenomes in model grass Brachypodium polyploids

We designed a subgenome detection pipeline (PhyloSD) that allowed us to identify the three known and four ghost diploid progenitor genomes of six grass Brachypodium allopolyploids, and to infer the hypothetical evolutionary scenarios for their origins. Our pipeline can be used with either transcriptome or genome data, and retrieves the progenitor subgenomes of both allopolyploid and autopolyploid species.