Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives
2011
Wicker, Thomas, T. | Mayer, Klaus F. X., K. F. X. | Gundlach, Heidrun, H. | Martis, Mihaela, M. | Steuernagel, Burkhard, B. | Scholz, Uwe, U. | Simkova, Hana, H. | Kubalakova, Marie, M. | Choulet, Frédéric | Taudien, Stefan, S. | Platzer, Matthias, M. | Feuillet, Catherine, C. | Fahima, Tzion, T. | Budak, Hikmet, H. | Dolezel, Jaroslav, J. | Keller, Beat, B. | Stein, Nils, N. | Inst Plant Biol ; Universität Zürich [Zürich] = University of Zurich (UZH) | Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences ; Helmholtz Zentrum München = German Research Center for Environmental Health (HMGU) | Ctr Reg Hana Biotechnol & Agr Res ; Inst Expt Bot | Génétique Diversité et Ecophysiologie des Céréales (GDEC) ; Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP) | Inst Evolut ; Ǧāmiʿat͏̈ Hayfā = University of Haifa | Fac Engn & Nat Sci ; Sabanci University [Istanbul] | German Ministry of Education and Research (BMBF) [FKZ 0314000, GABI-BARLEX]; Swiss National Science Foundation [3100A-127061/1]; Czech Republic Ministry of Education Youth and Sports [LC06004, OC08025]; Commissariat a l'Energie Atomique-Genoscope [AP2008]; Agence Nationale de la Recherche [ANR-GPLA06001G]; European Community [FP7-212019]; European Cooperation in Science and Technology [FA0604]
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.
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