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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.
Highlights
The tribe of Triticeae is within the subfamily of the Pooideae and comprises between 400–500 species including diploids and polyploids
Chloroplast genome assemblies A single run of 454 titanium 7 kb paired end sequencing was conducted on genomic DNA of 11 Triticeae species and subspecies (Table 1) and additional sequences for T. aestivum were provided by the University of Bristol
The assembly was hampered by the inverted repeat sequence (IR), which could not be resolved into two separate copies with the available sequences and would have required specific and time consuming laboratory procedures
Summary
The tribe of Triticeae is within the subfamily of the Pooideae and comprises between 400–500 species including diploids and polyploids It includes several major crop species such as, Hordeum vulgare (barley), Secale cereale (rye) and Triticum aestivum (wheat). These species have undergone many changes during the domestication process, with the domesticated taxa being distinct from their wild ancestors [1,2]. The D genome was added to the domesticated tetraploid T. dicoccon from Ae. tauschii approximately 8,000–10,000 years ago to form the complete hexaploid genome complement of T. aestivum [10,11,12,13]
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