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Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:507-32. [PMID: 27145194 DOI: 10.1111/tpj.13207] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 05/18/2023]
Abstract
The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.
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Affiliation(s)
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Daniel Gonzalez-Ibeas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Jeanne Whalen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Robin Paul
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | | | | | - Russell L Reagan
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sriema L Walawage
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Charis Cardeno
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kevin Pratt
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Sowmya Kuruganti
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | | | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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