121159 20240319081014.0 doi 10.1111/tpj.15650 sideral 131593 ART-2022-131593 eng Sancho, Rubén Universidad de Zaragoza (orcid)0000-0002-4845-4242 Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids 2022 Access copy available to the general public Unrestricted Unraveling 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. info:eu-repo/grantAgreement/ES/DGA-FSE/A01-17 info:eu-repo/grantAgreement/ES/DGA-FSE/A01-20R info:eu-repo/grantAgreement/ES/MICINN/CGL2016-79790-P info:eu-repo/grantAgreement/ES/MICINN/PID2019-108195GB-I00 info:eu-repo/grantAgreement/ES/UZ/UZ2016-TEC-02 info:eu-repo/semantics/openAccess by-nc-nd http://creativecommons.org/licenses/by-nc-nd/3.0/es/ 7.2 2022 PLANT SCIENCES 17 / 239 = 0.071 2022 Q1 T1 2.118 2022 Cell Biology 2022 Q1 Plant Science 2022 Q1 Genetics 2022 Q1 11.6 2022 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Inda, Luis A. Universidad de Zaragoza (orcid)0000-0002-1214-375X Díaz-Pérez, Antonio Des Marais, David L. Gordon, Sean Vogel, John P. Lusinska, Joanna Hasterok, Robert Contreras-Moreira, Bruno Universidad de Zaragoza (orcid)0000-0002-5462-907X Catalán, Pilar Universidad de Zaragoza (orcid)0000-0001-7793-5259 5011 063 Universidad de Zaragoza Dpto. CC.Agrar.y Medio Natural Área Botánica 109, 6 (2022), 1535-1558 Plant j. PLANT JOURNAL 0960-7412 6380785 http://zaguan.unizar.es/record/121159/files/texto_completo.pdf Versión publicada 2800218 http://zaguan.unizar.es/record/121159/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:121159 articulos driver 2024-03-18-15:28:58 ARTICLE