doi:10.1111/tpj.15650engSancho, RubénInda, Luis A.Díaz-Pérez, AntonioDes Marais, David L.Gordon, SeanVogel, John P.Lusinska, JoannaHasterok, RobertContreras-Moreira, BrunoCatalán, PilarTracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploidsART-2022-131593Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinctor unknown or when genome sequences of known progenitors are unavailable. Existing subgenome identi-fication methods cannot adequately infer the homeologous genomes that are present in the allopolyploidsif they do not take into account the potential existence of unknown progenitors. We addressed this chal-lenge in the widely distributed dysploid grass genusBrachypodium, which is a model genus for temperatecereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenomedetection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic sub-genome detection pipeline was validated inTriticumallopolyploids, which have known progenitor geno-mes, and then used to infer the identities of three subgenomes derived from extant diploid species and foursubgenomes derived from unknown diploid progenitors (ghost subgenomes) in sixBrachypodiumpolyplo-ids (B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestreandB. hybridum), of which fivecontain undescribed homeologous subgenomes. The existence of the sevenBrachypodiumprogenitor geno-mes in the polyploids was confirmed by their karyotypic barcode profiles. Comparative phylogenomics ofnuclear versus plastid trees allowed us to formulate hypothetical homoploid hybridizations and allo- andautopolyploidization scenarios that could have generated the sixBrachypodiumpolyploids.2022http://zaguan.unizar.es/record/12115910.1111/tpj.15650http://zaguan.unizar.es/record/121159oai:zaguan.unizar.es:121159info:eu-repo/grantAgreement/ES/DGA-FSE/A01-17info:eu-repo/grantAgreement/ES/DGA-FSE/A01-20Rinfo:eu-repo/grantAgreement/ES/MICINN/CGL2016-79790-Pinfo:eu-repo/grantAgreement/ES/MICINN/PID2019-108195GB-I00info:eu-repo/grantAgreement/ES/UZ/UZ2016-TEC-02PLANT JOURNAL 109, 6 (2022), 1535-1558by-nc-ndhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/info:eu-repo/semantics/openAccess