Schwacke Rainer, Bolger Marie E, Usadel Björn
Forschungszentrum Jülich, Institute of Bio- and Geosciences, IBG-4 Bioinformatics, CEPLAS, BioSC, Jülich, Germany.
Heinrich-Heine University Düsseldorf, Faculty of Mathematical and Natural Sciences, Institute for Biological Data Science, CEPLAS, Düsseldorf, Germany.
Front Plant Sci. 2025 Jun 24;16:1603547. doi: 10.3389/fpls.2025.1603547. eCollection 2025.
Advances in next-generation sequencing technologies over the last decade have substantially reduced the cost and effort required to sequence plant genomes. Whereas early efforts focused primarily on economically important crops and model species, attention has now turned to a broader range of plants, including those with larger and more complex genomes. In 2024, the genomes of 500 plant species were published, including 370 sequenced for the first time. Tracking and providing access to published plant genomes (now covering more than 1800 species) is an invaluable service for plant researchers. PubPlant is an online resource that serves this purpose by cataloging published plant genome sequences and offering multiple visualizations (https://www.plabipd.de/pubplant_main.html). It includes a chronology of genome publications, and cladograms to display the phylogenetic relationships among the sequenced plants. An overview diagram for seed plants highlights taxonomic orders and families with sequenced species and reveals those that have been overlooked thus far. As a use case for PubPlant, we evaluated the status of sequenced food crops. We found that the five plant families featuring the most food crops were those containing the most sequenced plant species.
在过去十年中，新一代测序技术的进步大幅降低了对植物基因组进行测序所需的成本和工作量。早期的工作主要集中在具有经济重要性的作物和模式物种上，而现在注意力已转向更广泛的植物，包括那些基因组更大、更复杂的植物。2024年，公布了500种植物的基因组，其中370种是首次测序。追踪并提供已公布的植物基因组（目前涵盖超过1800个物种）的访问权限，对植物研究人员来说是一项非常有价值的服务。PubPlant是一个在线资源，通过编目已公布的植物基因组序列并提供多种可视化方式来实现这一目的（https://www.plabipd.de/pubplant_main.html）。它包括基因组出版物年表，以及用于展示已测序植物之间系统发育关系的分支图。种子植物的概述图突出了有测序物种的分类目和科，并揭示了那些迄今为止被忽视的分类目和科。作为PubPlant的一个应用案例，我们评估了已测序粮食作物的状况。我们发现，拥有最多粮食作物的五个植物科也是拥有最多已测序植物物种的科。
