Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

María Muñoz-Amatriaín; Stefano Lonardi; 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

doi:10.1111/tpj.12959

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Plant J. 2015 Oct;84(1):216-27. doi: 10.1111/tpj.12959. Epub 2015 Sep 21.

Authors

María Muñoz-Amatriaín¹, Stefano Lonardi², MingCheng Luo³, Kavitha Madishetty¹, Jan T Svensson^{1

4}, Matthew J Moscou^{1

5}, Steve Wanamaker¹, Tao Jiang², Andris Kleinhofs⁶, Gary J Muehlbauer⁷, Roger P Wise⁸, Nils Stein⁹, Yaqin Ma^{1

3

10}, Edmundo Rodriguez^{1

11}, Dave Kudrna¹², Prasanna R Bhat^{1

13}, Shiaoman Chao¹⁴, Pascal Condamine¹, Shane Heinen⁷, Josh Resnik^{1

15}, Rod Wing¹², Heather N Witt^{3

16}, Matthew Alpert^{2

17}, Marco Beccuti^{2

18}, Serdar Bozdag^{2

19}, Francesca Cordero^{2

18}, Hamid Mirebrahim², Rachid Ounit², Yonghui Wu^{2

20}, Frank You^{21

22}, Jie Zheng^{2

23}, Hana Simková²⁴, Jaroslav Dolezel²⁴, Jane Grimwood^{25

26}, Jeremy Schmutz^{25

26}, Denisa Duma^{2

27}, Lothar Altschmied⁹, Tom Blake²⁸, Phil Bregitzer²⁹, Laurel Cooper^{30

31}, Muharrem Dilbirligi^{6

32}, Anders Falk³³, Leila Feiz^{28

34}, Andreas Graner⁹, Perry Gustafson³⁵, Patrick M Hayes³⁰, Peggy Lemaux³⁶, Jafar Mammadov^{37

38}, Timothy J Close¹

Affiliations

¹ Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
² Department of Computer Science, University of California, Riverside, CA, 92521, USA.
³ Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
⁴ Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden.
⁵ The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
⁶ Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
⁷ Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
⁸ Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA.
⁹ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
¹⁰ Molefarming Laboratory USA, Davis, CA, 95616, USA.
¹¹ Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México.
¹² Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA.
¹³ Monsanto Research Center, Bangalore, 560092, India.
¹⁴ USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA.
¹⁵ Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA.
¹⁶ Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
¹⁷ Turtle Rock Studios, Lake Forest, CA, 92630, USA.
¹⁸ Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy.
¹⁹ Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA.
²⁰ Google Inc., Mountain View, CA, 94043, USA.
²¹ USDA-ARS, Albany, CA, 94710, USA.
²² Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
²³ School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore.
²⁴ Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic.
²⁵ Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA.
²⁶ US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
²⁷ Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA.
²⁸ Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA.
²⁹ USDA-ARS, Aberdeen, ID, 83210, USA.
³⁰ Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
³¹ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
³² International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey.
³³ Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
³⁴ Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA.
³⁵ USDA, University of Missouri, Columbia, MO, 65211, USA.
³⁶ Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
³⁷ Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
³⁸ Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, 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: Aegilops tauschii; BAC sequencing; Barley; HarvEST:Barley; Hordeum vulgare L.; centromere BACs; gene distribution; recombination frequency; synteny.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes, Artificial, Bacterial / genetics*
Genome, Plant / genetics*
Hordeum / genetics*
Molecular Sequence Data

Associated data

GENBANK/AC250371
GENBANK/AC250421
GENBANK/AC250484
GENBANK/AC250784
GENBANK/AC251557
GENBANK/AC251639
GENBANK/AC251663
GENBANK/AC251805
GENBANK/AC251814
GENBANK/AC252228
GENBANK/AC252453
GENBANK/AC252497
GENBANK/AC252610
GENBANK/AC256237
GENBANK/AC256288
GENBANK/AC256303
GENBANK/AC269749