title: Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives.
abstract: All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
authors.affiliation: Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.forename: Mihaela
authors.initials: M
authors.lastname: Martis
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
authors.forename: Marie
authors.initials: M
authors.lastname: Kubaláková
authors.forename: Frédéric
authors.initials: F
authors.lastname: Choulet
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.forename: Tzion
authors.initials: T
authors.lastname: Fahima
authors.forename: Hikmet
authors.initials: H
authors.lastname: Budak
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Dolezel
authors.forename: Beat
authors.initials: B
authors.lastname: Keller
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
mesh_terms: D001483:Base Sequence; D058431:Brachypodium / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics*; D045868:Sorghum / Q000235:genetics; D026801:Synteny / Q000235:genetics; D014908:Triticum / Q000235:genetics*