Abstract

BackgroundTriticum 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.ResultsGenetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and Am-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.ConclusionsRNA-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.

Highlights

  • Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding

  • Since the phylogenetic tree confirmed the genome differentiation between the diploid species, we investigated the distribution of unique nucleotide substitutions over the chromosomes that discriminated between each of the genomes (Fig. 4 and Additional file S1: Fig. S4)

  • Clear differentiation between Ae. comosa and Ae. uniaristata despite their phenotypic similarity Our RNA sequencing (RNA-seq)-based phylogenetic analyses using singlenucleotide polymorphisms (SNPs) in nuclear and chloroplast genomes showed that Ae. uniaristata and Ae. comosa, belonging to the section Comopyrum, were the most closely related species among the diploid Triticum and Aegilops species

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Summary

Introduction

Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. The homoeologous chromosomes of the diploid genomes are distinguished by in situ hybridization patterns of highly repetitive sequences and C-banding patterns, indicating that genome differentiation of diploid wheat and its relatives manifests at least partly in the distribution of heterochromatin and the accumulation of highly repetitive sequences [6]. Certain repetitive sequences such as retrotransposons rapidly and dramatically increase in their copy numbers in evolutionary-specific lineages [7,8,9], implying that repetitive sequence-based approaches would not necessarily reflect genetic relationships among related species. The use of genome-wide exon sequences, should be considered for clarifying the evolutionary relationships among related genomes

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