RT Journal Article SR Electronic T1 High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome JF bioRxiv FD Cold Spring Harbor Laboratory SP 809798 DO 10.1101/809798 A1 Annarita Marrano A1 Monica Britton A1 Paulo A. Zaini A1 Aleksey V. Zimin A1 Rachael E. Workman A1 Daniela Puiu A1 Luca Bianco A1 Erica Adele Di Pierro A1 Brian J. Allen A1 Sandeep Chakraborty A1 Michela Troggio A1 Charles A. Leslie A1 Winston Timp A1 Abhaya Dandekar A1 Steven L. Salzberg A1 David B. Neale YR 2019 UL http://biorxiv.org/content/early/2019/10/17/809798.abstract AB 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, and the full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) are full-length, 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 catkin 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. Overall, Chandler v2.0 is a valuable resource to understand and explore walnut biology better.