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.
Highlights
In recent years, the genus Brachypodium has become one of the most comprehensively studied genera among monocotyledonous plants primarily due to the exploitation of one of its flagship species, B. distachyon, as a functional model organism for temperate cereals and other economically important grasses [1,2,3,4,5]
We adopted the nomenclature for the chromosomes of the Brachypodium perennials according to their alignment with CoGe, which is based on sequencing data for B. sylvaticum with reference to their assignment to B. distachyon
Our current analyses in several Brachypodium species enabled the dissection of their karyotype organization, tracking of the evolutionary histories of individual chromosomes, and the identification of an additional x = 5 genome (RABK, x = 5)
Summary
The genus Brachypodium has become one of the most comprehensively studied genera among monocotyledonous plants primarily due to the exploitation of one of its flagship species, B. distachyon, as a functional model organism for temperate cereals and other economically important grasses [1,2,3,4,5] It comprises three annuals, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20). One of the most widespread and best studied perennial species is B. sylvaticum which has considerable readily available genetic resources such as inbred lines, efficient transformation protocols, and genomic and transcriptomic tools Because of these, it has been recently proposed as a new model plant to study perenniality [3,7,18,19]. Given the economic importance of perennial grasses, comparative studies of more closely related Brachypodium annuals and perennials can be of particular importance in identifying and testing candidate “perenniality” genes and creating a tractable model system for both fundamental research and crop improvement [7,18]
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