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

被引:8
|
作者
Tanaka, Sayaka [1 ]
Yoshida, Kentaro [1 ]
Sato, Kazuhiro [2 ]
Takumi, Shigeo [1 ]
机构
[1] Kobe Univ, Grad Sch Agr Sci, Nada Ku, Rokkodai 1-1, Kobe, Hyogo 6578501, Japan
[2] Okayama Univ, Inst Plant Sci & Resources, Chuo 2-20-1, Kurashiki, Okayama 7100046, Japan
关键词
Genome-wide polymorphisms; Genome differentiation; RNA sequencing; Wheat; SINGLE NUCLEOTIDE POLYMORPHISMS; WILD WHEAT; LEAF TRANSCRIPTS; PLASMON ANALYSIS; TAUSCHII; CHROMOSOMES; PROGENITOR; CAUDATA;
D O I
10.1186/s12864-020-6664-3
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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.
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