title: 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.
authors.affiliation: Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Middleton
authors.affiliation: Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Switzerland.
authors.forename: Natacha
authors.initials: N
authors.lastname: Senerchia
authors.affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America.
authors.forename: Eduard D
authors.initials: ED
authors.lastname: Akhunov
authors.affiliation: Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
authors.forename: Beat
authors.initials: B
authors.lastname: Keller
authors.affiliation: Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.affiliation: Leibniz-Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kilian
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D054628:Genome, Chloroplast / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D001467:Hordeum / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011123:Polyploidy; D012434:Secale / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013997:Time Factors; D014908:Triticum / Q000235:genetics*