Mapping the genomic landscape of Prunus spp. with PrunusMap

IF 8.7 1区农林科学 Q1 Agricultural and Biological Sciences Horticulture Research Pub Date : 2024-10-24 DOI:10.1093/hr/uhae301

Najla Ksouri, María Ángeles Moreno, Bruno Contreras-Moreira, Yolanda Gogorcena

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Abstract

Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies (GWAS) 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.

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利用 PrunusMap 绘制梅花属植物的基因组图谱

下一代测序技术推动了植物育种工具的重大进步，如全基因组关联研究（GWAS）和单核苷酸多态性（SNP）分析。在这一动态环境中，包含 SNP 标记的植物数据库已发展成为促进育种计划和基因组研究的中心。PrunusMap（可在 https://prunusmap.eead.csic.es 上访问）是一个专为 Prunus 社区定制的开源网络应用程序。PrunusMap 拥有友好的用户界面，使用户能够无缝对齐和定位梅花品种和栽培品种多个基因组版本的标记，支持不同的查询和格式。除了定位标记位置外，它还提供了邻近基因和蛋白质注释的综合列表。这一简化流程由 "查找标记"、"对齐序列"、"对齐蛋白质 "和 "按位置定位 "四个直观功能驱动，大大减少了工作量，提高了效率，尤其适合生物信息学专业知识有限的用户。此外，PrunusMap 的多功能性还体现在它承诺根据用户要求纳入更多的梅花基因组序列、注释和标记。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Horticulture Research Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

11.20

自引率

6.90%

发文量

367

审稿时长

20 weeks

期刊介绍： Horticulture Research, an open access journal affiliated with Nanjing Agricultural University, has achieved the prestigious ranking of number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. As a leading publication in the field, the journal is dedicated to disseminating original research articles, comprehensive reviews, insightful perspectives, thought-provoking comments, and valuable correspondence articles and letters to the editor. Its scope encompasses all vital aspects of horticultural plants and disciplines, such as biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.