RNA-based Phylogenomics, Subgenome-Detection Algorithms and Cross-bracing Dating Approaches Reveal the Ancestry of Known and 'Ghost' Homeologous Subgenomes and their Hybridization Ages in Grass Brachypodium Allopolyploids

Subgenome identification methods could not adequately retrieve all the diploid homeologous genomes present in the allopolyploids if the searching algorithms do not take into account the potential existence of unknown progenitors. We have addressed this challenge in the widely dysploid grass model genus Brachypodium by using a transcriptome-based phylogeny and newly designed subgenome detection algorithms. We have inferred the identities of the subgenomes and the hybridization events that created six allopolyploid species, all of which but one contain unobserved diploid homeologous genomes. We have analysed cytogenetic and RNA-seq data from 11 diploid and polyploid Brachypodium species, including 12 accessions of which 10 (B. arbuscula, B. boissieri, B. hybridum, B. mexicanum, B. phoenicoides-Bpho6, B. phoenicoides-B422, B. pinnatum, B. retusum, B. rupestre and B. stacei) have been sequenced by RNA-seq, representing two thirds of the recognized taxa in the genus, which cover all the main splits and hybridization scenarios within its phylogeny.