Abstract
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.
Introduction
The first plant genome to be sequenced was that of the laboratory model Arabidopsis thaliana, published in the year 2000 (The Arabidopsis Genome Initiative, 2000). It took 10 further years to achieve the milestone of 20 sequenced plant genomes, but only another 4 years to pass 100 genomes, and by the year 2020 the milestone of 500 plant genomes had been achieved. Remarkably, 500 additional plant genomes were sequenced in the next 2 years (one tenth of the time needed for the first 500). This progress is still accelerating, mainly due to the advent of third-generation long-read sequencing technologies () and their continual refinement (; ). Advances in sequencing technologies have gone hand in hand with the development of more powerful bioinformatics algorithms for the assembly and annotation of genomic data. Genome assembly tools such as hifiasm () and verkko () can integrate data from the two most popular long-read sequencing technologies, namely nanopore sequencing developed by Oxford Nanopore Technologies and single-molecule real-time sequencing commercialized as the PacBio platform by Pacific Biosciences (van Rengs et al., 2022).
The advances in third-generation sequencing have reduced the cost and effort needed for genome sequencing to such a degree that it is now within the means of even moderately-funded research groups. It is therefore unsurprising that recent years have seen a dramatic increase in the number of plant whole-genome sequencing projects (Figure 1). By the end of 2024, more than 1800 plant species had been sequenced, more than 500 of which have been sequenced twice and more than 200 of which have been sequenced three or more times. The number of plant species that have been sequenced is increasing steadily, but the number of individual sequenced genomes is increasing at a much faster rate due to the re-sequencing of the same species multiple times. Re-sequencing is driven by the repetition of earlier sequencing efforts using more advanced technologies to obtain better and more complete genomes as well as intra-species pan-genome projects involving the sequencing of multiple individuals (such as different varieties, cultivars or ecotypes) within a species to explore the full genomic landscape (). Prominent examples of staple crop pan-genomes include maize (), barley (), wheat (), rice () and potato (Tang et al., 2022; ), as well as fruit crops such as tomato (; Zhou et al., 2022), and beverage crops such as tea (; Tariq et al., 2024).
Figure 1
The history of plant genome sequencing has been summarized at intervals to highlight the status of sequenced plant genomes at the time of publication, often focusing on particular technological advances (; ; ; Shirasawa et al., 2021; ; Sun et al., 2022; ). But such is the pace of change that such review articles are often out of date by the time they are published. One attempt to present a more frequently updated resource is the Plants-Genomes-Technologies (N3) database (Xie et al., 2024). The current iteration is version 3.0 (accessed February 17, 2025), which was published on January 11, 2024. Here, we describe an additional online resource called PubPlant (https://www.plabipd.de/pubplant_main.html) that has tracked and continuously updated published plant genome sequences for almost a decade.
Methods
Tracking published plant genomes
PubPlant tracks published plant genomes using manual search and curation methods. Searches are conducted using the Google search engine, cited reference searches in the Web of Science database (), and the NCBI PubMed citation database (). All search results are reviewed manually, and relevant information is extracted and entered into JavaScript Object Notation (JSON) files via copy and paste. These manually curated JSON files serve as the data source for the web-based diagrams that visualize the current status of sequenced plant genomes. The JSON source files also encode phylogenetic information, with taxonomic relationships based on the classifications listed in Table 1. Diagrams are generated client-side using a JavaScript script that employs the D3.js library (v4, https://d3js.org) for cladogram rendering, and the Vis.js library (v3.1, https://visjs.org) for the timeline visualizations.
Table 1
| Plant group | Classification |
|---|---|
| Angiosperms | APG-IV system (The Angiosperm Phylogeny Group, 2016; Zuntini et al., 2024) |
| Gymnosperms | Yang et al. (2022) |
| Lycophytes and ferns | PPG-I system (The Pteridophyte Phylogeny Group, 2016; ) |
| Bryophytes | |
| Primary algae | |
| Others | NCBI Taxonomy (Schoch et al., 2020); |
Resources used for phylogenetic classification in the diagrams presented by PubPlant.
To be included in PubPlant, the sequenced genome must belong to a plant (from the Archaeplastida group, which includes land plants, charophytes, green algae, glaucophytes, red algae and Rhodelphidophyta) and must be comprehensively described in a peer-reviewed journal. This means that the reads must be assembled into contigs, the contigs must have undergone scaffolding, and structural gene annotation must be completed. Accordingly, PubPlant excludes highly fragmented genomes or those with incomplete or missing structural annotations.
If a publication includes the genomes of multiple accessions representing a single species, such as an intra-species pan-genome, PubPlant counts the species as sequenced and published once. If a pan-genome is based on the genomes of different species – often described as a super pan-genome () – each species is counted individually. The accepted scientific names of vascular plant species are cross-checked against (). The lowest recognized taxonomic rank is the species. Accordingly, genomes of different subspecies or varieties are pooled.
Food crops
All statistical data concerning major food crop species were extracted from the Food and Agriculture Organization Corporate Statistical Database (). The data provided by FAOSTAT refer to crop categories with an annual production of more than 5000 tons in 2022. Each of these categories contains one or several food crops. The NCBI Taxonomy Database (Schoch et al., 2020) was used to assign correct scientific names to individual crops.
Results and discussion
Chronology of published plant genomes
PubPlant’s timeline view displays sequenced plant genomes according to the chronology of their first publication dates (Figure 2, a full list of published plant genomes is presented in Supplementary Table 1). If there are two publications for the same plant species on the same date, the publication with the earliest acceptance date is listed. The timeline view groups the plant entries as belonging to dicotyledons, non-dicotyledons, non-angiosperms or algae (Figure 2).
Figure 2
Phylogeny of sequenced plant genomes
PubPlant’s cladogram view arranges published plant genomes according to the phylogenetic position of each species (Figure 3). The cladograms for flowering and non-flowering plants are displayed separately to improve legibility. Each entry in the cladogram provides a mouse-over function that displays a popup box containing the scientific name, common name and genome size of the plant. Publication details (one or more publications), including links to the corresponding full-text articles, are also provided in the popup box.
Figure 3
Overview diagram of sequenced seed plants
The two major groups of seed plants are the angiosperms and gymnosperms. Angiosperms are by far the most diverse extant plant group, comprising more than 350,000 known species assigned to more than 400 families in 64 orders. The gymnosperms are a much smaller group, containing only 1100 living species, which is comparable to some of the larger angiosperm genera (e.g., Solanum, Acacia and Rhododendron) in terms of species numbers. By the end of 2024, 1700 angiosperm species and 26 gymnosperm species had been sequenced.
While the cladogram diagrams in PubPlant focus at the individual species level, the overview diagram provides a view at the taxonomic family level using an embedded progress bar. The cladogram displays the phylogenetic position of each plant family while the progress bar depicts the number of sequenced species in that family (Figure 4). The overview diagram also includes families lacking any sequenced species thus far. This reveals that there are many plant families with no sequenced species (e.g., 25 of 38 families in the order Caryophyllales).
Figure 4
Use case: sequenced food crops
As a use case, we evaluated the current status of sequenced food crops. Economically important food crop plants have always been a major target for sequencing efforts because this provides information about the genes responsible for agronomically favorable traits. The enormous genome sizes of some of these crops, mainly due to polyploidy, the presence of repetitive DNA () and very long introns (Xu et al., 2024), hindered progress until the advent of long-read sequencing (). For example, the sizes of the onion and broad bean genomes are 16 Gbp () and 13 Gbp (), respectively. But thanks to the advances mentioned earlier, almost all of the food crop species listed in the FAOSTAT database () have now been sequenced.
Further analysis of the most highly sequenced plant families (Poaceae, Fabaceae, Solanaceae, Rosaceae and Brassicaceae) indicated that these also contain the largest number of food crop species (Figure 5, listed in Table 2). Other families such as Salicaceae, which do not contain any food crops, also may have sequenced species, but this reflects the numerous poplar and willow species in that family, which are important to the timber industry. Similarly, many species of Orchidaceae have been sequenced (Figure 5) despite the presence of only one crop species (vanilla), due to the economic importance of many orchids as ornamental plants.
Figure 5
Table 2
| Taxonomic family | Plants with sequenced genomes a | Food crop species with sequenced genomes a,b |
|---|---|---|
| Poaceae | 141 species | Sugar cane Saccharum x sp. Maize/corn Zea mays Wheat Triticum aestivum Rice Oryza sativa Barley Hordeum vulgare Sorghum Sorghum bicolor Millet Setaria italica, Panicum miliaceum, Cenchrus americanus, Eleusine coracana Oat Avena sativa Rye Secale cereale Fonio millet Digitaria exilis |
| Fabaceae | 129 species | Soybean Glycine max Groundnut Arachis hypogaea Pea Pisum sativum Chickpea Cicer arietinum Cowpea Vigna unguiculata Broad bean Vicia faba Pigeon pea Cajanus cajan Lentil Lens culinaris Lupins Lupinus albus, Lupinus angustifolius Common (string) bean Phaseolus vulgaris Vetch Vicia sativa Bambara bean Vigna subterranea Locust bean Ceratonia siliqua |
| Rosaceae | 91 species | Apple Malus domestica Peach and nectarine Prunus persica Pears Pyrus communis, Pyrus pyrifolia Plum and sloe Prunus domestica Strawberry Fragaria x ananassa Apricot Prunus armeniaca Almond Prunus dulcis Cherry Prunus avium Sour cherry Prunus cerasus Raspberry Rubus idaeus Quince Cydonia oblonga |
| Solanaceae | 119 species | Potato Solanum tuberosum Tomato Solanum lycopersicum Eggplant Solanum melongena Chilies and peppers Capsicum annuum, Capsicum frutescens, Capsicum chinense, Capsicum baccatum, Capsicum pubescens |
| Brassicaceae | 88 species | Cabbages Brassica oleracea, Brassica rapa Rapeseed Brassica napus Mustard Sinapis alba, Brassica nigra, Brassica juncea Other vegetables Raphanus sativus, Eruca sativa, Lepidium sativum, Eutrema japonicum, Armoracia rusticana |
Plant families with the highest numbers of sequenced genomes.
Evaluated in February 2025.
Food crop categories according to FAOSTAT database.
Only a few food crops remain to be sequenced (Table 3), including several culinary spices belonging to the Apiaceae (e.g. anise), leek (Amaryllidaceae), gooseberry and currants (Grossulariaceae). Notably, the blackcurrant (Grossulariaceae) is one of the most recently sequenced crop plants (Ziegler et al., 2024). Almost all of the food crops yet to be sequenced rank in the bottom half of the top 120 food crops ordered by production quantity (Table 3). Although all important food crop plants have now been sequenced, the remaining unsequenced species tend to be important in countries that contribute less to plant genome sequencing (Table 3). The countries that have contributed the most to the publication of crop plant genomes are China, the USA, Japan, Germany and Australia (Xie et al., 2024).
Table 3
| Food crop category a | Ranking by production quantity b | Total production quantity (kiloton) | Main producers by production quantity (production share) c | Current status in genome sequencing d |
|---|---|---|---|---|
| Anise, badian, coriander, cumin, caraway, fennel, juniper berries Pimpinella anisum Illicium verum Coriandrum sativum Cuminum cyminum Carum carvi Foeniculum vulgare Juniperus communis | 76th | 2751 | India (68.6%) Turkey (12.6%) | not sequenced (except Coriandrum sativum) |
| Leek Allium ampeloprasum | 80th | 2109 | Indonesia (30.3%) Turkey (8.0%) | not sequenced |
| Yerba Maté Ilex paraguariensis | 82nd | 1653 | Argentina (56.3%) Brazil (37.4%) | sequenced (Vignale et al., 2025) |
| Currants Ribes nigrum Ribes rubrum | 97th | 764 | Russian Fed. (66.6%) Poland (19.1%) | Ribes nigrum sequenced (Ziegler et al., 2024) |
| Yautía Xanthosoma sagittifolium | 103rd | 396 | Cuba (22.7%) Venezuela (22.3%) | not sequenced |
| Kola nuts Cola acuminata Cola nitida | 104th | 315 | Nigeria (55.3%) Côte d’Ivoire (18.6%) | not sequenced |
| Gooseberry Ribes uva-crispa | 112th | 95 | Russian Fed. (89.0%) Ukraine (8.0%) | not sequenced |
| Brazil nut Bertholletia excelsa | 113th | 79 | Brazil (48.1%) Bolivia (42.9%) | sequenced (Wang et al., 2025) |
| Locust bean Ceratonia siliqua | 114th | 56 | Turkey (44.5%) Morocco (39.1%) | sequenced () |
| Peppermint, spearmint Mentha x piperita Mentha spicata | 115th | 51 | Morocco (84.0%) Argentina (13.7%) | Mentha x piperita Sequenced (Talbot et al., 2024) |
Food crop plants that have not been sequenced, or have been sequenced very recently.
Food crop categories according to the FAOSTAT database.
Ranking among the top 120 food crop categories (data for 2022).
Top two countries with the largest share of world production (data for 2022).
Evaluated in February 2025.
Conclusion
In recent years, the publication of newly sequenced plant genomes has increased to such an extent that it has become a weekly event (Figure 1). Periodic review articles provide a snapshot of the situation at the time the manuscripts were written but are quickly outdated. We therefore seek to highlight the online resource PubPlant, which provides up-to-date information on published plant genomes. PubPlant features a timeline view, where sequenced plant genomes are arranged in chronological order by the date of first publication (Figure 2), and a cladogram view, showing all sequenced plant species arranged according to their phylogeny (Figure 3). Separate cladograms are provided to display the phylogenetic positions of sequenced flowering and non-flowering plants. A summary diagram shows the phylogenetic position of all sequenced seed plants down to the taxonomic family rank, including those without any species sequenced thus far. It shows the total number of species for each family, the number of sequenced species, and the sequenced genera, while highlighting recently published genomes (Figure 4).
As a use case for PubPlant, we evaluated the status of sequenced food crop plants, which tend to be prioritized for genome sequencing. Unsurprisingly, almost all major food crop species (FAOSTAT food crop categories ranked by production quantity, full list in Supplementary Table 2) have already been sequenced. In addition, the five plant families with the greatest number of sequenced plant genomes (Poaceae, Fabaceae, Rosaceae, Solanaceae and Brassicaceae) are also those containing the most major food crop species (Table 2).
PubPlant has been available online for more than 9 years and has been widely used, including as a resource to prepare review articles summarizing plant genome sequencing progress (; ; ) and to evaluate the status of sequenced medicinal plants (). Whereas other plant genome resources release irregular updates, PubPlant is updated on a monthly basis, providing a simple and intuitive source of current and historical information on sequenced plant genomes for the benefit of the entire plant research community.
Statements
Data availability statement
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
Author contributions
RS: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing, Resources. MB: Conceptualization, Methodology, Supervision, Validation, Writing – original draft, Writing – review & editing, Funding acquisition. BU: Project administration, Supervision, Writing – original draft, Writing – review & editing, Funding acquisition.
Funding
The author(s) declare that financial support was received for the research and/or publication of this article. RS, MB and BU are supported by the German Federal Ministry of Research, Technology and Space (BMFTR) in the frame of the German Network for Bioinformatics Infrastructure (de.NBI).
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Generative AI statement
The author(s) declare that no Generative AI was used in the creation of this manuscript.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2025.1603547/full#supplementary-material
Supplementary Table 1List of published sequenced plant genomes in chronological order.
Supplementary Table 2List of food crop categories (FAOSTAT) ranked by production quantity.
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Summary
Keywords
sequenced plant genomes, plant genome publication, timeline, cladogram, Archaeplastida
Citation
Schwacke R, Bolger ME and Usadel B (2025) PubPlant – a continuously updated online resource for sequenced and published plant genomes. Front. Plant Sci. 16:1603547. doi: 10.3389/fpls.2025.1603547
Received
31 March 2025
Accepted
02 June 2025
Published
24 June 2025
Volume
16 - 2025
Edited by
Guang-Long Wang, Huaiyin Institute of Technology, China
Reviewed by
Aureliano Bombarely, Polytechnic University of Valencia, Spain
Kang Zhang, Chinese Academy of Agricultural Sciences, China
Updates
Copyright
© 2025 Schwacke, Bolger and Usadel.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Rainer Schwacke, r.schwacke@fz-juelich.de
Disclaimer
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