High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome
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Abstract
Background
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.
Findings
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%) present both start and stop codons, which represents a significant improvement compared with 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 intraspecies 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.
Conclusion
Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
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Now published in GigaScience doi: 10.1093/gigascience/giaa050
Annarita Marrano 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: amarrano@ucdavis.eduMonica Britton 2Bioinformatics Core Facility, Genome Center, University of California Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaulo A. Zaini 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAleksey V. Zimin 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on …
Now published in GigaScience doi: 10.1093/gigascience/giaa050
Annarita Marrano 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: amarrano@ucdavis.eduMonica Britton 2Bioinformatics Core Facility, Genome Center, University of California Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaulo A. Zaini 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAleksey V. Zimin 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRachael E. Workman 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDaniela Puiu 4Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuca Bianco 5Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach, San Michele all’ Adige (TN) 38010, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca BiancoErica Adele Di Pierro 5Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach, San Michele all’ Adige (TN) 38010, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBrian J. Allen 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSandeep Chakraborty 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichela Troggio 5Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach, San Michele all’ Adige (TN) 38010, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCharles A. Leslie 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWinston Timp 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Winston TimpAbhaya Dandekar 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven L. Salzberg 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA4Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA6Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid B. Neale 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa050 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102235 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102236
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