ArticleGigaScience2020
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed, 138 citations in OpenAlex.
- Out of the blue: family-wide loss of anthocyanin biosynthesis in Cucurbitaceae.The Plant journal : for cell and molecular biology · 2026Article
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- Landscape Genomic Tools Can Inform Future Rootstock and Farmland Selection for an Agricultural Tree Nut From Its Wild Relatives.Molecular ecology · 2026Article
- Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon.Nature genetics · 2026Article
- Genome degradation in plant tissue culture.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Using reciprocally retained gene families to detect whole-genome multiplications in plants.Genome biology · 2026Article
- The Walnut's Dark Secret: Polyphenol Oxidase and the Enigmatic Pathway to Melanin.International journal of molecular sciences · 2026Review
- Resolving sampling and population-size biases in domestication genomics supports a South Asian origin of walnuts.Genome biology · 2026Article
- The Mechanism of TT2-TypePlants (Basel, Switzerland) · 2025Article
- Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts.Current biology : CB · 2025Article
- Analysis of genetic differences underlying chilling stress tolerance using whole genome Re-Sequencing in walnut (Juglans regia L.).BMC genomics · 2025Article
- Comparative Transcriptome Analysis of Walnuts (Plants (Basel, Switzerland) · 2025Article
- Genome-wide identification, transcriptome dynamics, and expression regulation of the key lignin biosynthesis gene families PAL and CAD in black walnut shell.BMC plant biology · 2025Article
- Identification and functional characterization of JrbZIP40 in walnut reveals its role in salt and drought stress tolerance in transgenic Arabidopsis seedlings.BMC plant biology · 2025Article
- Metagenomic analysis reveals Bacillus cereus OTU8977 as a potential probiotic in promoting walnut growth.BMC plant biology · 2025Article
- Genomic insights into genome-wide heterozygosity and its impact on walnut adaptive evolution and improvement.Molecular breeding : new strategies in plant improvement · 2025Article
- Genetic Mechanisms and Adaptive Benefits of Anthocyanin Red Stigmas in a Wind-Pollinated Tree.Molecular biology and evolution · 2025Article
- Genome-wide association study dissects the genetic architecture of progesterone content in Persian walnut leaves (Juglans regia L.).BMC genomics · 2025Article
- Integrated analysis of the transcriptome and hormone metabolome elucidates the regulatory mechanisms governing walnut bud germination.BMC genomics · 2025Article
- Leveraging Walnut Somatic Embryos as a Biomanufacturing Platform for Recombinant Proteins and Metabolites.Biotech (Basel (Switzerland)) · 2024Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundThe 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.
findingsHere, 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.
conclusionOverall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.