Summary
Resource Type
Organism
Abbreviation
J. regia
Genus
Juglans
Species
regia
Common Name
English Walnut
Cross Reference
Description

Order: Fagales
Family: Juglandaceae
Chromosome Number: 2n=32
Draft Genome Sequence
David Neale and Charles Langley (UC Davis) worked with the California Walnut Board to sequence the walnut genome, currently released as v2.0. A manuscript is expected soon. Links:

Reference Genome V2
The newest version of the J. regia genome, available for download. Annotation coming soon.

Publication: Coming soon.

Reference Genome V1.5
Stevens et al. produced draft genomes for Juglans regia, five additional Juglans species (J. nigra, J. sigillata, J. microcarpa, J. catheyensis, and J. hindsii) and the related species Pterocarya stenoptera. This J. regia assembly is not annotated and is available for download only.

Publication: Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH. Genomic Variation Among and Within Six Juglans Species. G3 (Bethesda). 2018 May 23. pii: g3.200030.2018. doi: 10.1534/g3.118.200030.

Reference Genome V1
The original, fully annotated reference genome for J. regia from Martínez‐García et al. All searchable genes currently come from this version. Available for searching, downloading, browsing and BLAST.

Publication: Martínez‐García PJ, Crepeau MW, Puiu D, Gonzalez‐Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols. The Plant Journal. 2016 May 1.

Genetic and Physical Map
Publication: Luo MC, You FM, Li P, Wang JR, Zhu T, Dandekar AM, Leslie CA, Aradhya M, McGuire PE, Dvorak J. Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC genomics. 2015 Sep 17;16(1):1.

Reference Genome
NameProgramDate Constructed
Juglans regia - Reference Genome V 1.0Newbler (Roche) [18-Jan-2017]Aug 20th, 2018
Juglans regia - Reference Genome V 2.0Long read Hi-C scaffoldingDec 11th, 2018
Draft reference genomes for six Juglans species and Pterocarya stenopteraTrinity, MUMmer, SamtoolsJun 14th, 2018
JBrowse

The English Walnut (Juglans regia) Jbrowse instance corresponds to the v 1.0 reference genome assembly. The Black Walnut (Juglans nigra) variants track were generated using GMAP.

Total J. nigra mrna contigs Contigs mapped to J. regia >90% identity >90% coverage
78,834 74,984 68,235 62,387

Go to JBrowse

Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Juglans regia - peptides InterProScanInterProScanJan 19th, 2017
Juglans regia - mRNA BLASTX against SwissProtblastxJan 19th, 2017
Juglans regia - Reference Genome V 1.0Newbler (Roche) [18-Jan-2017]Aug 20th, 2018
Draft reference genomes for six Juglans species and Pterocarya stenopteraTrinity, MUMmer, SamtoolsJun 14th, 2018
Juglans regia - Reference Genome V 2.0Long read Hi-C scaffoldingDec 11th, 2018
Gene Ontology Browser
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KEGG Browser
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