Mapping the genomic landscape of Prunus spp. with PrunusMap

Abstract

Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source Web application tailored for the Prunus community. Featuring a user-friendly interface, PrunusMap empowers users to seamlessly align and locate markers across multiple genome versions of Prunus species and cultivars, supporting different queries and formats. Beyond locating marker positions, it provides a comprehensive list of annotated nearby genes and proteins. This streamlined process, driven by four intuitive features ‘Find markers’, ‘Align sequences’, ‘Align proteins’, and ‘Locate by position’, significantly reduces workload and boosts efficiency, particularly for users with limited bioinformatics expertise. Moreover, PrunusMap’s versatility is underscored by its commitment to incorporate additional Prunus genome sequences, annotations, and markers upon user request.The authors would like to thank Dr Veronica Guajardo for providing data on ‘Adafuel’ SNPs and Bixente Sehabiague for his technical assistance. This work was funded by CSIC [grants 2020AEP119 & FAS2022_052], the Spanish Research Agency [grants AGL2017-83358-R & PID2023-146749OB-I00, funded by MCIN/AEI/10.13039/501100011033 ‘A way of making Europe’] and the Government of Aragón [grants A44, A09_23R, A10_23R, and PhD contract to Najla Ksouri 2018–2023], which were cofinanced with FEDER fundsPublishe