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

Abstract

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 genomewide 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.

Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences

“…The comparative single-gene FISH analysis highlighted the role of karyotype changes in the evolution of closely related C-, M- and U-genomes of Aegilops . Recent phylogenomic studies on diploid Triticum / Aegilops species using 38 nuclear low copy loci (Huynh et al, 2019 ) and by genome-wide RNA-seq-based polymorphic analysis (Glémin et al, 2019 ; Tanaka et al, 2020 ) have shown that the ancestor of the D-genome lineage went through intensive diversification ~3 Mya, leading to the formation of the current Aegilops species with C, D, M, N, S, and U genomes in the area of Fertile Crescent and their subsequent radiation to the Mediterranean landscapes (Kilian et al, 2011 ). Glémin et al ( 2019 ) and Tanaka et al ( 2020 ) suggested that C-, M-, N-, and U-genome species formed a separated group from those containing the D and S genomes.…”

“…comosa and the N genome of Ae. uniaristata (Glémin et al, 2019 ; Tanaka et al, 2020 ). Consistent with these results, the single-gene FISH map of Ae.…”

RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species

“…comosa (MM genome), and Ae. uniaristata (NN genome) (Tanaka et al 2020). RNA-Seq of these diploid species allowed us to detect genomewide SNPs and indels across chromosomes.…”

“…The efficient generation of markers in several Triticeae species prompted us to analyze genome differentiation in diploid wild wheat by applying RNA-Seq to wild wheat species with more diverse diploid genomes. We estimated genome differentiation based on an RNA-Seq-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops (Tanaka et al (2020). The genome nomenclatures in these species were defined based on their affinity for chromosomal pairing.…”

“…However, balancing economic importance and sequencing costs for the analysis of wild wheat species is an ongoing challenge. RNA-Seq has provided a valuable source of information for identifying polymorphisms in wild wheat accessions for use in genetic and evolutionary studies (Glémin et al 2019;Miki et al 2019;Tanaka et al 2020), even when reference genomes for these species were not available and Ae. tauschii or barley diploid genomes were used to determine the genomes' physical structures.…”