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Background   Triticum  and  Aegilops  diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus  Aegilops :  Ae. caudata  L. (CC genome),  Ae. comosa  Sibth. et Sm. (MM genome), and  Ae. uniaristata  Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of  Triticum  and  Aegilops .    Results  Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and A m -genomes.  Ae. caudata  had the second highest genetic diversity following  Ae. speltoides , the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid  Triticum  and  Aegilops  species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.    Conclusions  RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid  Triticum  and  Aegilops  species and supported the chromosome-pairing-based genome nomenclature system, except for the position of  Ae. speltoides . Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

bmc genomics

Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops