Pan genome resources for grapevine

K. Chougule, M.K. Tello-Ruiz, S. Wei, A. Olson, Z. Lu, S. Kumari, V. Kumar, B. Contreras-Moreira, G. Naamati, S. Dyer, I. Papatheodorou, N. George, J. Elser, S. Naithani, P. Jaiswal, D. Ware
Capturing and characterizing the gene space within a species and linking to agronomic traits will be critical to improving agricultural practices and accelerating crop improvement. Recent advances in genome sequencing and assembly technologies are now making it possible to generate many accurate high quality reference genome assemblies for each species. The grapevine community is no longer limited to the single PN40024 reference assembly, but has access to many high-quality reference assemblies for table and wine grapes. With this increase in the number of genomes, there is a need to integrate the information to support the transition from single reference to pan-genome research approaches. Here, we present a pan-genome resource for grapevine ( that includes 10 reference genomes representing wild and cultivated grape genomes. In addition, there are seven genomes as outgroups that provide a powerful phylogenetic framework constructed with 594,645 input proteins from 553,999 individual genes, resulting in 24,050 protein-coding gene family trees of which 8,881 are grapevine specific. PN40024 V3 was used as a reference genome for gene expression and orthology-based pathway projections. This resource allows exploration of pan-gene sets for the species, characterizing potential gene gain and loss between different accessions of grapevine reference assemblies based on the gene trees.
Chougule, K., Tello-Ruiz, M.K., Wei, S., Olson, A., Lu, Z., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., Dyer, S., Papatheodorou, I., George, N., Elser, J., Naithani, S., Jaiswal, P. and Ware, D. (2024). Pan genome resources for grapevine. Acta Hortic. 1390, 257-266
DOI: 10.17660/ActaHortic.2024.1390.31
pan-genome, comparative genomics, Ensembl, phylogenetic analysis, gene tree, genetic variation, Expression Atlas, Gramene, Plant Reactome

Acta Horticulturae