Supporting data for "High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome"

Dataset type: Genomic, Transcriptomic
Data released on April 20, 2020

Marrano A; Britton M; Zaini PA; Zimin AV; Workman RE; Puiu D; Bianco L; Di Pierro EA; Allen BJ; Chakraborty S; Troggio M; Leslie CA; Timp W; Dandekar A; Salzberg SL; Neale DB (2020): Supporting data for "High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome" GigaScience Database. http://dx.doi.org/10.5524/100735

DOI10.5524/100735

The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes.
Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) presents both start and stop codons, which represents a significant improvement compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome scale genome facilitates in-depth studies of intra-species genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars.
Overall, Chandler v2.0 will serve as a valuable resource to understand and explore walnut biology better.

Additional details

Read the peer-reviewed publication(s):


Additional information:

https://www.hardwoodgenomics.org/Genome-assembly/2539069

Accessions (data generated as part of this study):

BioProject: PRJNA291087





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Jr_R051240 English walnutJuglans regia Description:RNA extracted from the somatic embryo ...
Common name:English walnut
Alternative accession-BioSample:SAMN12783437
...
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Jr_R151240 English walnutJuglans regia Description:RNA extracted from the leaves of an En...
Common name:English walnut
Alternative accession-BioSample:SAMN12783438
...
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Jr_R251240 English walnutJuglans regia Description:RNA extracted from the shoot of an Eng...
Common name:English walnut
Alternative accession-BioSample:SAMN12783439
...
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Jr_R351240 English walnutJuglans regia Description:RNA extracted from the callus of an En...
Common name:English walnut
Alternative accession-BioSample:SAMN12783440
...
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Jr_R451240 English walnutJuglans regia Description:RNA extracted from the root of an Engl...
Common name:English walnut
Alternative accession-BioSample:SAMN12783441
...
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Jr_R551240 English walnutJuglans regia Description:RNA extracted from a 1-inch elongated ...
Common name:English walnut
Alternative accession-BioSample:SAMN12783442
...
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Jr_R651240 English walnutJuglans regia Description:RNA extracted from a 3-inch elongated ...
Common name:English walnut
Alternative accession-BioSample:SAMN12783443
...
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Jr_R751240 English walnutJuglans regia Description:RNA extracted from the pollen of an En...
Common name:English walnut
Alternative accession-BioSample:SAMN12783444
...
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Jr_R851240 English walnutJuglans regia Description:RNA extracted from the pistillate flow...
Common name:English walnut
Alternative accession-BioSample:SAMN12783445
...
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SAMN0370423551240 English walnutJuglans regia Description:DNA extracted from the leaves of an 18...
Common name:English walnut
Alternative accession-BioSample:SAMN03704235
...
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Displaying 1-10 of 10 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsBAM1.42 GB2020-04-11
AlignmentsBAM1.99 GB2020-04-11
AlignmentsBAM1.71 GB2020-04-11
AlignmentsBAM1.06 GB2020-04-11
AlignmentsBAM3.14 GB2020-04-11
AlignmentsBAM1.75 GB2020-04-11
AlignmentsBAM2.74 GB2020-04-11
AlignmentsBAM1.4 GB2020-04-11
AlignmentsBAM1.73 GB2020-04-11
AlignmentsBAM1.78 GB2020-04-11
Displaying 1-10 of 45 File(s).
Funding body Awardee Award ID Comments
California Walnut Board D B Neale D-0417-22
California Walnut Board D B Neale D-0418-22
Date Action
April 20, 2020 Dataset publish
April 24, 2020 Manuscript Link added : 10.1093/gigascience/giaa050