Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops

Abstract

Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.

Keywords: RNA sequencing; chromosomal synteny; genome differentiation; genome-wide polymorphisms; wheat.

Figure 1

Bar charts illustrating the number of SNPs (A) and indels (B) between the B genome of T. aestivum cv. Chinese Spring and each of the 19 accessions of section Sitopsis species.

Figure 2

Distribution of SNPs (A) and indels (B) between the T. aestivum cv. Chinese Spring (CS) B genome and each of the 19 accessions of section Sitopsis species on the physical map of the CS B genome. From outer to inner circle, CS B genome (scale in Mb) and chromosome number (black), Ae. speltoides ssp. ligustica KU-2236, KU-7716, and KU-7848 (red); Ae. spletoides ssp. speltoides KU-2208A, KU-14601, KU-14605, and KU-12963a (orange); Ae. longissima KU-5752, KU-14624, and KU-14635 (green); Ae. searsii KU-5755, KU-6142, KU-6143, and KU-14651 (blue); Ae. sharonensis KU-14661, KU-14663, and KU-14668 (purple); and Ae. bicornis KU-5784 and KU-14613 (grey).

Figure 3

Phylogenetic relationship among the 19 accessions of section Sitopsis species (S genome), the B genomes of T. aestivum cv. Chinese Spring and T. turgidum ssp. durum cv. Langdon, T. urartu (A genome), Ae. tauschii (D genome), and Ae. umbellulata (U genome). NJ tree (A) and phylogenetic network (B) are shown. Bootstrap probabilities are shown on the branches (number of bootstrap replications = 1000). The scale bar is shown below each phylogenetic tree.

Figure 4

Distributions of the positions of fixed nucleotide differences between subspecies of Aegilops speltoides ssp. ligustica and Ae. spletoides ssp. speltoides (A) and between Ae. sharonensis and Ae. longissima (B) on the physical map of the B genome of T. aestivum cv. Chinese Spring from chromosomes 1B to 7B.

Figure 5

Irregular topologies of the phylogenetic trees in the distal chromosomal regions. The chromosomal regions were divided into 86 segments of 60 Mbp each. NJ trees were constructed based on non-redundant SNPs located in each segment. Squares on the chromosomes in panel (A) correspond to the 86 segments. Phylogenetic trees of the white squares showed that the B genome of T. aestivum cv. Chinese Spring was the most closely related to Ae. speltoides in the section Sitopsis. This observation was consistent with those for trees constructed based on all non-redudnant SNPs (Fig. 5). Phylogenetic trees of the black squares showed that the B genome was closely related to Emarginata clades. A phylogenetic tree of the grey square showed that the B genome was located outside of Sitopsis species. Trees with irregular topologies at the end of the long arm of chromosome 1B (B) and the short arm (C) and long arm (D) of chromosome 3B are shown. Bootstrap probabilities with over 50% and scale bars are shown for each tree.

Figure 6

Contrasting pattern of nucleotide divergence in the distal and proximal regions of B-genome chromosomes. Average number of nucleotide differences per 20 Mbp between species in Truncata (=Ae. speltoides spp.) and the B genome of T. aestivum cv. Chinese Spring (D_T-B) and between Emarginata species and the B genome (D_E-B) are plotted on each chromosome. The distributions of these differences are shown by line graphs (orange and green) in the top panels. Area charts in grey colour in the top panels denote the distribution of the total number of non-redundant SNPs per 20 Mbp in Sitopsis species and the B genome. Middle panels show the distribution of the ratio expressing disparity between the two genetic divergences ([D_E-B − D_T-B] × 100/D_T-B) along each chromosome using bar charts. Area charts in blue colour indicate the distribution of the number of genes along each chromosome.