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

Sancho, Rubén (Universidad de Zaragoza) ; Inda, Luis A. (Universidad de Zaragoza) ; Díaz-Pérez, Antonio ; Des Marais, David L. ; Gordon, Sean ; Vogel, John P. ; Lusinska, Joanna ; Hasterok, Robert ; Contreras-Moreira, Bruno (Universidad de Zaragoza) ; Catalán, Pilar (Universidad de Zaragoza)

Resumen: 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.

Idioma: Inglés

DOI: 10.1111/tpj.15650

Año: 2022

Publicado en: PLANT JOURNAL 109, 6 (2022), 1535-1558
ISSN: 0960-7412

Factor impacto JCR: 7.2 (2022)

Categ. JCR: PLANT SCIENCES rank: 17 / 239 = 0.071 (2022) - Q1 - T1

Factor impacto CITESCORE: 11.6 - Biochemistry, Genetics and Molecular Biology (Q1) - Agricultural and Biological Sciences (Q1)

Factor impacto SCIMAGO: 2.118 - Cell Biology (Q1) - Plant Science (Q1) - Genetics (Q1)

Financiación: info:eu-repo/grantAgreement/ES/DGA-FSE/A01-17
Financiación: info:eu-repo/grantAgreement/ES/DGA-FSE/A01-20R
Financiación: info:eu-repo/grantAgreement/ES/MICINN/CGL2016-79790-P
Financiación: info:eu-repo/grantAgreement/ES/MICINN/PID2019-108195GB-I00
Financiación: info:eu-repo/grantAgreement/ES/UZ/UZ2016-TEC-02

Tipo y forma: Artículo (Versión definitiva)

Área (Departamento): Área Botánica (Dpto. CC.Agrar.y Medio Natural)