Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

Abstract

Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.

Long noncoding miRNA gene represses wheat β-diketone waxes

“…Barley, which contains diketone wax but in which there are no reports of a dominant wax inhibitor gene, diverged from wheat 8-12 Mya, suggesting that the inverted duplication event that created Iw occurred after this date (74)(75)(76)(77). The inverted duplication may have been a single event in an ancestral wheat genome lineage or separate later events resulting in convergent evolution in B (Iw1) and D (Iw2) genome species.…”

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

“…42, Supplementary Table 5 and Supplementary Note). In contrast, their hosts-rye and wheat, respectively-had already diverged approximately 4 million years ago 9 . This incongruence in the divergence times of a host and pathogen can be due to host tracking: until a few hundreds of thousands of years ago, wheat and rye were still in the host range of a single forma specialis, and divergence into two distinct formae speciales occurred only relatively recently.…”

“…tritici and B. graminis f. sp. hordei diverged approximately 6 million years ago 4 , whereas their hosts, wheat and barley, respectively, diverged at least 2 million years earlier 9 . An alternative explanation could be a recent host jump from wheat to rye or vice versa, followed by the rapid emergence of barriers to gene flow.…”

Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen

“…These studies also showed that Bgh and Bgt became reproductively isolated 6.3 million (±1.1 million) years ago, which is after the divergence of the sister Triticeae species barley and wheat (8 million to 9 million years ago; ref. 19). Estimates of the divergence time of the alternating isolate-specific monomorphic and polymorphic regions in both Bgh and Bgt genomes are >5,000 y, implying that these genome mosaics are the product of rare outbreeding events (by sexual reproduction) followed by frequent asexual (clonal) reproduction, which maintains the haploid genome structure in the respective pathogen populations.…”