Major structural genomic alterations are associated with hybrid speciation in Aegilops markgrafii (Triticeae)

Most grasses of the tribe Triticeae have syntenic chromosomes except for a few species with rearranged genomes. Aegilops markgrafii (2n=14), a diploid wild relative of wheat has highly asymmetrical chromosomes indicative of many chromosomal rearrangements have reshaped its genome. Molecular cytogenetics and next generation sequencing were used to explore genome organization and speciation. We applied fluorescence in situ hybridization (FISH) with a set of 101 physically mapped wheat cDNA markers to establish the Ae. markgrafii chromosome macrostructure and homoeologous relationships. Two chromosomes were found colinear and maintained cross genome synteny whereas the rest were highly rearranged as a result of inter- and intrachromosomal translocations and inversions. Location of near-centromeric cDNAs and centromeric repeats showed that the centromeres were not involved in rearrangements. To investigate the relationship between chromosomal alterations and the patterns of molecular evolution in the rearranged fractions of the Ae. markgrafii chromosomes, we characterized the genome using shallow whole-genome shotgun sequencing and whole exome capture. The composition of transposable elements was established and their distribution along the chromosomes was studied by FISH. The pattern of some dispersed repeats reflected the chromosomal rearrangements and differentiated chromosomal blocks with diverse phylogenetic affinity. Comparative analysis of Ae. markgrafii, barley and hexaploid wheat orthologous gene sequences revealed rearranged chromosomal blocks with different levels of sequence divergence suggesting their origin from different parental genomes associated with hybrid speciation.