Draft reference genomes for six Juglans species and Pterocarya stenoptera

Summary

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.
Name	Draft reference genomes for six Juglans species and Pterocarya stenoptera
Resource Type	Genome Assembly
Organism	J. cathayensis (Chinese Walnut) J. sigillata (Iron Walnut) J. regia (English Walnut) J. nigra (Black Walnut) J. hindsii (Northern California Black Walnut) P. stenoptera (Chinese wingnut) J. microcarpa (Texas Black Walnut)

Details

Program, Pipeline, Workflow or Method Name	Trinity, MUMmer, Samtools
Program Version	n/a
Date Performed	Thursday, June 14, 2018 - 17:00
Data Source

Description and Download

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. The J. regia assembly below is not annotated and is not the primary genome Download assembled data:

	Juglans sigillata Genome Assembly (fasta format)
	Juglans sigillata CDS (fasta format)
	Juglans sigillata Polypeptides (fasta format)
	Juglans microcarpa Genome Assembly (fasta format)
	Juglans hindsii Genome Assembly (fasta format)
	Juglans hindsii CDS (fasta format)
	Juglans hindsii Polypeptides (fasta format)
	Juglans nigra Genome Assembly (fasta format)
	Juglans nigra CDS (fasta format)
	Juglans nigra Polypeptides (fasta format)
	Juglans cathayensis Genome Assembly (fasta format)
	Juglans cathayensis CDS (fasta format)
	Juglans cathayensis Polypeptides (fasta format)
	Pterocarya stenoptera Genome Assembly (fasta format)
	Pterocarya stenoptera CDS (fasta format)
	Pterocarya stenoptera Polypeptides (fasta format)

Stevens et al. performed a reassembly of J. regia with new PacBio reads. This is provided as a supplement to their paper, but as it is not annotated, it is not hosted as the primary J.regia reference genome.

	Juglans regia 1.5 Genome Assembly (fasta format)

Download aligned reads (VCF):

	Juglans regia Variant calls (VCF format)
	Juglans nigra Variant calls (VCF format)
	Juglans hindsli Variant calls (VCF format)
	Juglans microcarpa Variant calls (VCF format)

Draft reference genomes for six Juglans species and Pterocarya stenoptera

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