Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids

Abstract

Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when their progenitor genome sequences are unavailable. The subgenome identification methods cannot adequately retrieve the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate cereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenome detection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic subgenome detection pipeline was validated in Triticum allopolyploids, which have known progenitor genomes, and was used to infer the identities of three extant and four ghost subgenomes in six Brachypodium polyploids (B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestre and B. hybridum), of which five contain undescribed homeologous subgenomes. The existence of the seven Brachypodium progenitor genomes in the polyploids was confirmed by their karyotypic barcode profiles. Our results demonstrate that our subgenome detection method is able to uncover the ancestral genomic components of both allo- and autopolyploids.

Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes

“…Unlike autopolyploids, allopolyploids contain multiple divergent subgenomes, each derived from distinct parental species. The investigation of subgenome evolution has been propelled by recent advances in homoeology analyses ( Glover et al 2016 ; Sancho et al 2021 ). From modeling and inference perspectives, allopolyploidy is of particular interest, as it results from hybridization of two species and gives rise to evolutionary histories in the form of phylogenetic networks.…”