Summary
Publication
Marrano, A., Britton, M., Zaini, P. A., Zimin, A. V., Workman, R. E., Puiu, D., ... & Troggio, M. (2020). High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. GigaScience, 9(5), giaa050.
Name
Juglans regia - Reference Genome V 2.0
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
Long read Hi-C scaffolding
Program Version
n/a
Date Performed
Tuesday, December 11, 2018 - 14:40
Data Source
Description and Download

Reference Genome v2.0

The release of the first reference genome sequence of Persian walnut (Chandler v1.0; Martínez-García et al., 2016) has been crucial for the discovery of millions of variants and the development of the AxiomTM J. regia 700K SNP genotyping array (Marrano et al., 2018). However, Chandler v1.0 is highly fragmented. Here, Marrano et al. provide a chromosome-level genome assembly of walnut (Chandler v2.0; Marrano et al., accpeted), using Oxford Nanopore MinION sequencing and Hi-C scaffolding strategy. The release of the second reference genome sequence of Persian walnut (Chandler v2.0; Marrano et al.) High-quality chromosome-scale assembly of the walnut (Juglans regia L.) was published May 2020.

Visit the gene features and JBrowse from Version 1 of the reference genome.

Embargo

The authors are currently working on a manuscript reporting in detail methods and results of the new chromosome-level genome assembly of walnut (Marrano et al.). Therefore, the open access of Chandler v2.0 is protected by the data-use policy statements of the Ft Lauderdale and Toronto agreements.

Contact information

Contact David B. Neale at dbneale@ucdavis.edu
Contact Annarita Marrano at amarrano@ucdavis.edu

Downloads
Genome Scaffolds v2.0 (091219)
Transcripts v2.0 - Fasta file
CDS v2.0 - Fasta file
Protein v2.0 - Fasta file
Gene Annotation v2.0 - Nuclear - revised 12_2019 - GFF3 file
Gene Annotation - Mitochondria - v2.0 revised 12_2019 - GFF3 file
Gene Annotation - Plastid - v2.0 revised 12_2019 - GFF3 file
Functional Annotation
Functional annotation - mitochondria (2020_02)
Functional annotation - nuclear (2020_02)
Functional annotation - plastid (2020_02)

SNP Genotyping - Marrano et al, "High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome".

Publication

A. Marrano, M. Britton, A. Zaini, A. Zimin, R. Workman, D. Puiu, L. Bianco, E. Pierro, B. Allen, S. Chakraborty, M. Troggio, C. Leslie, W. Timp, A. Dandekar, S. Salzberg and D. Neale. High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome. Submitted.

Downloads
SNPs VCF File
Polymorphisms VCF File

SNP Genotyping - Marrano et al, "Deciphering of the genetic control of phenology, yield and pellicle color in Persian walnut (Juglans regia L.)"

The new AxiomTM J. regia 700K SNP genotyping array (Marrano et al., 2018) has been applied to genotype a large collection of over 1,200 walnut trees from the Walnut Improvement Program of the University of California - Davis. The availability of these valuable genotypic resources enabled to apply gene-tagging approaches for several traits of interest in Persian walnut, such as water use efficiency (Famula et al., 2019) and phenology (Marrano et al.).

Publication

Marrano A., Sideli G.M., Leslie C.A., Cheng H. & Neale D.B. Deciphering of the genetic control of phenology, yield and pellicle color in Persian walnut (Juglans regia L.).

Downloads
SNPs VCF File
Contact information

Contact Annarita Marrano at amarrano@ucdavis.edu


SNP Genotyping - Famula et al, "Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L."

Randi Famula has completed SNP genotyping of 60 indviduals from a breeding population of Juglans regia. A JBrowse track and other features to explore this data are coming soon.

Publication

Famula, R.A., Richards, J.A., Famula, T.R., & Neale, D.B. (2018). Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L. Tree Genetics & Genomes.

Downloads
VCF File
Contact information

Contact Randi Famula at rafamula@ucdavis.edu

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