Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

Abstract

The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodium distachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time.

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

“…The karyotypes of the previously unstudied B. arbuscula (2n=18), B. boissieri (2n=48) and B. retusum (2n=32) species were analyzed using CCB mapping as was described in Lusinska et al (2019). The mapping was done with reference to the B. distachyon karyotype and its genome was compared to the ancestral rice genome (IBI, 2010).…”

“…The karyotypic pattern of this species was revealed to be the same as that of the genomes of the core perennial clade diploids B. sylvaticum and B. pinnatum with x=9 (fig. 6; Lusinska et al 2019). B. arbuscula chromosomes Ba1, Ba2, Ba4, Ba6, Ba7, Ba8 and Ba9, which correspond, respectively, to the ancestral Oryza sativa Os1, Os3, Os2, Os7, Os6, Os5 and Os4 chromosomes did not undergo any fusions, whereas one nested chromosome fusion (NCF) of Os8 and Os10 was observed on chromosome Ba3 and two NCFs of Os12+Os9+Os11 on chromosome Ba5 (fig.…”

“…The arrows link the inferred (sub)genomes and karyotypes of each studied Brachypodium polyploid. The karyotype models are based on the CCB analysis of the B. arbuscula (2x), B. retusum (4x) and B. boissieri (6x) species that were analyzed in this study and other Brachypodium representatives that had been previously studied (Lusinska et al 2018; Lusinska et al 2019; Gordon et al 2020). Within the karyotypes, each chromosome or homoeologous chromosome region corresponded to the relevant ancestral rice chromosome equivalents (Os1-Os12; Os – Oryza sativa ) (IBI 2010).…”

“…The bar diagrams represent the frequencies of the homeologs in each polyploid and their assignments to the homeologous subgenomes (table 1B). that were analyzed in this study and other Brachypodium representatives that had been previously studied (Lusinska et al 2018;Lusinska et al 2019;Gordon et al 2020). Within the karyotypes, each chromosome or homoeologous chromosome region corresponded to…”

“…These computational approaches were validated using fluorescence in situ hybridization (FISH)-based comparative chromosome barcoding (CCB), which enables the specific painting of whole chromosomes or their regions. The CCB proved to be effective in tracking the structural and evolutionary trajectories of individual chromosomes and whole karyotypes in some dicots, (e.g., Arabidopsis thaliana and its relatives; Lysak et al 2006) and monocots (e.g., rice; Hou et al 2018) and recently contributed to dissecting the karyotype organization of some Brachypodium species (Lusinska et al 2019). Here, this combined phylogenomic and cytomolecular strategy enabled us to propose hypotheses about the identities of the known and unobserved progenitor genome donors in the studied Brachypodium polyploid species and to infer their times of origin.…”