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Sequencing of 15 622 gene‐bearing BACs clarifies the gene‐dense regions of the barley genome
Authors:MingCheng Luo  Kavitha Madishetty  Jan T Svensson  Matthew J Moscou  Steve Wanamaker  Tao Jiang  Andris Kleinhofs  Gary J Muehlbauer  Roger P Wise  Nils Stein  Yaqin Ma  Edmundo Rodriguez  Dave Kudrna  Prasanna R Bhat  Shiaoman Chao  Pascal Condamine  Shane Heinen  Josh Resnik  Rod Wing  Heather N Witt  Matthew Alpert  Marco Beccuti  Serdar Bozdag  Francesca Cordero  Hamid Mirebrahim  Rachid Ounit  Yonghui Wu  Frank You  Jie Zheng  Hana Simková  Jaroslav Dolezel  Jane Grimwood  Jeremy Schmutz  Denisa Duma  Lothar Altschmied  Tom Blake  Phil Bregitzer  Laurel Cooper  Muharrem Dilbirligi  Anders Falk  Leila Feiz  Andreas Graner  Perry Gustafson  Patrick M Hayes  Peggy Lemaux  Jafar Mammadov  Timothy J Close
Institution:1. Department of Plant Sciences, University of California, Davis, CA, USA;2. Department of Botany and Plant Sciences, University of California, Riverside, CA, USA;3. Nordic Genetic Resource Center, Alnarp, Sweden;4. The Sainsbury Laboratory, Norwich Research Park, Norwich, UK;5. Department of Computer Science, University of California, Riverside, CA, USA;6. Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA;7. Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA;8. Corn Insects and Crop Genetics Research, USDA‐Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA;9. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany;10. Molefarming Laboratory USA, Davis, CA, USA;11. Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Saltillo, Coah, México;12. Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA;13. Monsanto Research Center, Bangalore, India;14. USDA‐ARS Biosciences Research Lab, Fargo, ND, USA;15. Ronald Reagan UCLA Medical Center, Los Angeles, CA, USA;16. Keck School of Medicine, University of Southern California, Los Angeles, CA, USA;17. Turtle Rock Studios, Lake Forest, CA, USA;18. Department of Computer Science, University of Turin, Turin, Italy;19. Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA;20. Google Inc., Mountain View, CA, USA;21. USDA‐ARS, Albany, CA, USA;22. Agriculture and Agri‐Food Canada, Morden, MB, Canada;23. School of Computer Engineering, Nanyang Technological University, Singapore, Singapore;24. Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic;25. Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, USA;26. US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA;27. Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA;28. Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA;29. USDA‐ARS, Aberdeen, ID, USA;30. Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA;31. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA;32. International Cooperation Department, The Scientific and Technological Research Council of Turkey, Kavaklidere, Ankara, Turkey;33. Swedish University of Agricultural Sciences, Uppsala, Sweden;34. Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA;35. USDA, University of Missouri, Columbia, MO, USA;36. Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA;37. Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, USA;38. Dow AgroSciences LLC, Indianapolis, IN, USA
Abstract:Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole‐genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene‐containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical‐mapped gene‐bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene‐enriched BACs and are characterized by high recombination rates, there are also gene‐dense regions with suppressed recombination. We made use of published map‐anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D‐genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map‐based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene‐dense but low recombination is particularly relevant.
Keywords:Barley  Hordeum vulgare L    BAC sequencing  gene distribution  recombination frequency  synteny  centromere BACs  HarvEST:Barley     Aegilops tauschii   
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