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
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Genome Scaffolds v2.0 (091219)
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Transcripts v2.0 - Fasta file
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CDS v2.0 - Fasta file
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Protein v2.0 - Fasta file
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Gene Annotation v2.0 - Nuclear - revised 12_2019 - GFF3 file
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Gene Annotation - Mitochondria - v2.0 revised 12_2019 - GFF3 file
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Gene Annotation - Plastid - v2.0 revised 12_2019 - GFF3 file
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Functional Annotation
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Functional annotation - mitochondria (2020_02)
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Functional annotation - nuclear (2020_02)
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Functional annotation - plastid (2020_02)
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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
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SNPs VCF File
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Polymorphisms VCF File
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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
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
Contact information
Contact Randi Famula at rafamula@ucdavis.edu
