LGRPv2: A high‐value platform for the advancement of Fabaceae genomics

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Plant Biotechnology Journal Pub Date : 2025-06-23 DOI:10.1111/pbi.70220

Zijian Yu, Tianyu Lei, Xin Yi, Ya'nan Hao, Shengdan Wu, Zejia Xiao, Jiahui Qu, Shiyu Li, Li Wang, Yuxian Li, Lan Zhang, Yuxin Pan, Yidan Wang, Lixia Gou, Yuannian Jiao, Jinpeng Wang

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引用次数: 0

Abstract

SummaryFabaceae, as one of the most diverse angiosperm families, plays a crucial role in maintaining global ecosystems and advancing human civilization. With the rapid accumulation of legume genomes, we developed LGRPv2 (https://fabaceae.cgrpoee.top), an updated version of the Legume Genomics Research Platform. LGRPv2 integrates 413 genomes, covering all published legume genomes and containing our latest deciphered Tamarindus indica genome from early‐diverging legumes and three outgroup genomes (Euscaphis pleiosperma, Vitis vinifera, and Platycodon tenuifolia). It features user‐friendly interactive interfaces for studying functional annotations, gene duplications, regulatory proteins, N6‐methyladenosine modifications, and transposable elements. For easily exploring genome evolution associated with polyploidizations, we incorporated DotView, SynView, and DecoBrowse with genome synteny (GenS) to establish a central GenS database for legumes. Specialized web services for ancestral legume genomes enable scientists to analyse the role of paleogenome reshuffling in shaping genomic diversity. The platform offers 184 511 synteny‐based orthogroups and 1 086 836 genes from 139 families, and tools to explore agronomic trait origins. LGRPv2 integrates 40 550 transcriptomes, 5091 pan‐genomes, 12 136 metabolomes, species encyclopaedias, ecological resources, and literature for exploring legume genomics comprehensively. Furthermore, LGRPv2 implemented 58 window‐based operating tools (31 new) to efficiently support new mining, especially in advancing assembling pipelines for polyploidization identification, ancestral genome reconstruction, and gene family evolution. Finally, we provided detailed usage guides and community support to empower LGRPv2 with user‐friendly and continuously updated features.

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LGRPv2：豆科植物基因组学研究的高价值平台

豆科植物是被子植物中种类最多的科之一，在维护全球生态系统和促进人类文明方面发挥着至关重要的作用。随着豆类基因组的快速积累，我们开发了LGRPv2 (https://fabaceae.cgrpoee.top)，这是豆类基因组学研究平台的更新版本。LGRPv2整合了413个基因组，涵盖了所有已发表的豆科植物基因组，并包含了我们最新破译的早期分化豆科植物柽柳基因组和三个外群基因组（Euscaphis pleiosperma， Vitis vinifera和Platycodon tenuifolia）。它具有用户友好的交互界面，用于研究功能注释，基因复制，调节蛋白，N6甲基腺苷修饰和转座元件。为了方便地探索与多倍体化相关的基因组进化，我们将DotView、SynView和DecoBrowse与基因组synteny （GenS）结合在一起，建立了一个豆科植物的中央基因组数据库。专门的豆类祖先基因组网络服务使科学家能够分析古基因组重组在形成基因组多样性中的作用。该平台提供了来自139个家族的184 511个基于同音性的正系群和1 086 836个基因，以及探索农艺性状起源的工具。LGRPv2整合了40550个转录组，5091个泛基因组，12136个代谢组，物种百科全书，生态资源和文献，全面探索豆类基因组学。此外，LGRPv2实现了58个基于窗口的操作工具（31个新工具），以有效支持新的采矿，特别是在推进多倍体鉴定、祖先基因组重建和基因家族进化的组装管道中。最后，我们提供了详细的使用指南和社区支持，使LGRPv2具有用户友好和不断更新的功能。

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

Plant Biotechnology Journal 生物-生物工程与应用微生物

CiteScore

20.50

自引率

2.90%

发文量

201

审稿时长

1 months

期刊介绍： Plant Biotechnology Journal aspires to publish original research and insightful reviews of high impact, authored by prominent researchers in applied plant science. The journal places a special emphasis on molecular plant sciences and their practical applications through plant biotechnology. Our goal is to establish a platform for showcasing significant advances in the field, encompassing curiosity-driven studies with potential applications, strategic research in plant biotechnology, scientific analysis of crucial issues for the beneficial utilization of plant sciences, and assessments of the performance of plant biotechnology products in practical applications.