title: The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.
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.
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Martínez-García
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.
authors.forename: Marc W
authors.initials: MW
authors.lastname: Crepeau
authors.affiliation: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gonzalez-Ibeas
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA.
authors.forename: Jeanne
authors.initials: J
authors.lastname: Whalen
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.
authors.forename: Kristian A
authors.initials: KA
authors.lastname: Stevens
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA.
authors.forename: Robin
authors.initials: R
authors.lastname: Paul
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Timothy S
authors.initials: TS
authors.lastname: Butterfield
authors.affiliation: UC Davis Genome Center, Davis, CA, 95616, USA.
authors.forename: Monica T
authors.initials: MT
authors.lastname: Britton
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Russell L
authors.initials: RL
authors.lastname: Reagan
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Chakraborty
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Sriema L
authors.initials: SL
authors.lastname: Walawage
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Hans A
authors.initials: HA
authors.lastname: Vasquez-Gross
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.
authors.forename: Charis
authors.initials: C
authors.lastname: Cardeno
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Randi A
authors.initials: RA
authors.lastname: Famula
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Pratt
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA.
authors.forename: Sowmya
authors.initials: S
authors.lastname: Kuruganti
authors.affiliation: USDA National Clonal Germplasm Repository, Davis, CA, 95616, USA.
authors.forename: Mallikarjuna K
authors.initials: MK
authors.lastname: Aradhya
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Leslie
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors.forename: Abhaya M
authors.initials: AM
authors.lastname: Dandekar
authors.affiliation: 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.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA.
authors.forename: Jill L
authors.initials: JL
authors.lastname: Wegrzyn
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. dbneale@ucdavis.edu.
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
mesh_terms: D004156:Catechol Oxidase / Q000378:metabolism; D018745:Genome, Plant / Q000235:genetics*; D031324:Juglans / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D059808:Polyphenols / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D059808:Polyphenols; D004156:Catechol Oxidase
keywords: Juglans regia; gallolyl glucose transferase; genome assembly; polyphenol oxidase; polyphenols; whole-genome shotgun