High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

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.

Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

“…Each physical position of the identified MTAs was investigated to explore the extension of the surrounding linkage disequilibrium (LD) blocks using “solid spine of LD” method implemented in HaploView v4.2 software ( Barrett et al, 2005 ). We searched the defined LD blocks for candidate genes using the walnut nuclear gene annotation and mapped into the new chromosome-scale reference “Chandler” genome v2.0 ( Marrano et al, 2020 ) 2 .…”

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

“… a – c , Genome contiguity ( a ) and library coverage ( b ) demonstrate that the v5 release is a very complete genome and that it is among the best available plant reference genomes ( c ), compared to maize 128 durum wheat 129 , broomcorn millet 130 , teff 131 , poplar 132 , soybean 70 , cotton 47 , walnut 133 and strawberry 46 . d , Complete collinearity between marker order in both crosses (number of markers = 4,701) of a 4-way mapping population is evident.…”

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

“…An entire protein sequence of common walnuts was downloaded from NCBI (https:// www.ncbi.nlm.nih.gov/genome/?term=Juglans+regia accessed on 20 December 2020) [41]. Arabidopsis WRKY family members were downloaded from the Arabidopsis Information Resource website (TAIR, https://www.arabidopsis.org/index.jsp accessed on 21 December 2020) using a basic local alignment search tool (BLAST) to search for prevalent walnut protein sequences, including the Arabidopsis WRKY sequence as a query sequence while considering those with an E value less than 1 × 10 −10 as a typical walnut WRKY sequence.…”