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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
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.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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Kumagai LB, LeVesque CS, Blomquist CL, Madishetty K, Guo Y, Woods PW, Rooney-Latham S, Rascoe J, Gallindo T, Schnabel D, Polek M. First Report of Candidatus Liberibacter asiaticus Associated with Citrus Huanglongbing in California. Plant Dis 2013; 97:283. [PMID: 30722341 DOI: 10.1094/pdis-09-12-0845-pdn] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Huanglongbing (HLB), also known as citrus greening, is one of the most destructive citrus diseases worldwide and is seen as a major threat to the multimillion dollar citrus industry in California. The vector of the two bacterial species associated with this disease, Candidatus Liberibacter asiaticus and Ca. L. americanus, is the Asian citrus psyllid (ACP), Diaphorina citri (4). ACP was detected in California in August of 2008 and has since been detected in nine counties in southern California. As part of a long term survey and testing program for the ACP carrying the HLB associated bacteria, groups of ACP nymphs and adults were submitted to the Jerry Dimitman Citrus Research Board/Citrus Pest and Disease Prevention Program Laboratory in Riverside, CA. In March 2012, DNA extracted using the Qiagen MagAttract 96 DNA plant kit (QIAGEN Inc., 27220 Turnberry Lane, Suite 200, Valencia, CA 91355) from a group of three ACP adults tested positive for Ca. L. asiaticus with the real-time PCR assay developed by Li et al. (4). ACP adults were collected from a residential citrus tree located in the Hacienda Heights area of Los Angeles County, California. The approximately 1.8 meter tall lemon tree had 23 graft unions, primarily of lemon (Citrus × meyeri) and pomelo (Citrus maxima) varieties. The tree was unthrifty, with yellow shoots and chlorotic leaves. Symptoms on the lemon and pomelo leaves included asymmetrical blotchy mottling, yellowing, and corking of the leaf veins, with the blotchy mottle more prominent in the pomelo leaves. Pomelo leaves appeared crinkled along the thickened veins. Lemon leaves had yellow veins and a few had islands of green tissue completely surrounded by yellow tissue. The entire tree was removed, cut into sections, bagged, and transported to the CDFA Plant Pest Diagnostics Lab for analysis. Two hundred milligrams of petiole and midrib tissue from leaves apical to each graft union was collected, and DNA from each sample was extracted using the Qiagen DNeasy plant mini kit. DNA extracted from both lemon and pomelo leaves tested positive for Ca. L. asiaticus using real-time PCR (4). A 1,160-bp fragment of the 16S ribosomal RNA gene was amplified from the insect and plant DNA extracts using conventional PCR with primers Ol1 and OI2c (2). A 703-bp fragment of the β-operon gene was amplified from the insect and plant extracts with primers A2 and J5 (1). The 16S rDNA fragments from the insect and plant respectively (GenBank Accession Nos. JX430434 and JX455745) and the β-operon fragments (JX430435 and JX455746) showed 100% identity with the corresponding regions of Ca. L. asiaticus (CP001677) strain psy 62. Our 16S rDNA sequence showed 98% identity with Ca. L. africanus (EU921620), 97% identity with Ca. L. solanacearum (HM246509), and 96% with Ca. L. americanus (FJ036892). In response to the detection of HLB, a 241 km2 quarantine area around the detection site was established. Surveys for ACP and symptomatic host plants within the HLB quarantine area are ongoing. To date, there have been no additional positive detections. In the United States, HLB was first detected in Florida in 2005 (4) and in Texas in January of 2012 (3). To our knowledge, this is the first confirmed report of Ca. L. asiaticus associated with HLB in California. References: (1) A. Hocquellet et al. Mol. Cell. Probes 13:373, 1999. (2) S. Jagoueix et al. Mol. Cell. Probes 10:43, 1996. (3) M. Kunta et al. Phytopathology 102:S4.66, 2012. (4) W. Li et al. J. Microbiol. Methods 66:104, 2006.
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Affiliation(s)
- L B Kumagai
- California Department of Food and Agriculture (CDFA), Sacramento, CA 95832
| | - C S LeVesque
- Jerry Dimitman Citrus Research Board/Citrus Pest Disease Prevention Program Lab, Riverside, CA 92507
| | - C L Blomquist
- California Department of Food and Agriculture (CDFA), Sacramento, CA 95832
| | - K Madishetty
- Jerry Dimitman Citrus Research Board/Citrus Pest Disease Prevention Program Lab, Riverside, CA 92507
| | - Y Guo
- California Department of Food and Agriculture (CDFA), Sacramento, CA 95832
| | - P W Woods
- California Department of Food and Agriculture (CDFA), Sacramento, CA 95832
| | - S Rooney-Latham
- California Department of Food and Agriculture (CDFA), Sacramento, CA 95832
| | - J Rascoe
- USDA APHIS PPQ CPHST, Beltsville, MD 20705
| | - T Gallindo
- California Department of Food and Agriculture, San Gabriel, CA 91776
| | - D Schnabel
- California Department of Food and Agriculture (CDFA), Sacramento, CA 95832
| | - M Polek
- Jerry Dimitman Citrus Research Board/Citrus Pest Disease Prevention Program Lab, Riverside, CA 92507
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