PubPlant: The Google Maps of Plant DNA

Imagine trying to develop a new aircraft without blueprints or treat a disease without at least an anatomical atlas and physiological manuals of the human body. Plant breeders have faced these types of challenges until not long ago, trying to achieve higher yields, better nutrition, and stress resistance, often without genomic data to guide them. Today, advances in genome sequencing technologies allow researchers to build complete genetic maps of plants, which serve as a powerful new foundation for their work.

Building on this progress, Rainer Schwacke of Forschungszentrum Jülich from Germany, in collaboration with his colleagues Marie Bolger and Björn Usadel, developed PubPlant: a bioinformatics tool that promises to be the new “Google Maps” of plant DNA. This open-access, monthly-updated database centralizes and organizes the growing mountain of plant genomic information, allowing scientists, breeders, and biotechnologists to navigate—literally—through genomes with greater ease and precision. They can now leverage the “GPS” that takes them to the specific region of plant DNA where work must be done to breed a particular agronomic or nutritional trait. The team published this work in Frontiers in Plant Science.

“Think of it like a field atlas for plants. Instead of driving from farm to farm to check what’s growing, you can open one map and instantly see the layout. PubPlant does the same with plant genomes: It shows how published species are organized and related, so researchers and students can quickly find which plants are published allowing them to quickly see the relevant publications, and indirectly, the data,” Bolger wrote in an email.

But when the seeds of PubPlant were planted almost a decade ago, it wasn’t as a grand global initiative. “This was initially started as an internal project to keep track of published plant genomes for our automated plant protein annotation tool Mercator4,” said Schwacke via email. “It was quickly realized that there was no other reliable resource which provided this service (which we needed), so that motivated us to add this visualization to our website.”

Genomic Boom: Exponential Growth in Plant Genome Sequencing

Since the complete plant genome of Arabidopsis thaliana—a model species in plant biology, equivalent to the lab mouse in biomedical research—was published in 2000, the field of plant genomics has expanded at an unprecedented pace.² In the following 20 years, researchers sequenced 500 plant species. Then, in just two years between 2020 and 2022, they sequenced another 500—what once took two decades achieved in a fraction of the time.

In 2024, the pace quickened further: over 500 new genomes were published in a single year, 370 of which belonged to species that had never been sequenced before. This acceleration has been possible thanks to advances in third-generation sequencing technologies, greater international collaboration, and the reduction of what were once enormous costs.^3-4

With these numbers in mind, the challenge is no longer just sequencing more genomes but organizing, integrating, and exploiting this information in useful ways so that it can be used in applied research and public-private efforts in plant breeding.⁵

“Researchers and breeders often struggle to access and compare plant genomic resources spread across different repositories,” explained Bolger. “PubPlant streamlines this by providing a centralized user-friendly platform that informs users about available data and highlights under-sampled taxa. These can help with both scientific discovery and agricultural innovation.”

A Genomic Atlas for Plants

To bring order to the chaotic flood of information, the team built features in PubPlant to allow users to search, visualize, and filter plant genomes according to multiple criteria: species, taxonomic family, publication year, assembly quality, and more—all with direct links to scientific articles and original databases. The PubPlant team hopes that through interactive graphics and user-friendly interface, their website can transform scattered data into a navigable and usable resource.

“What makes this platform particularly distinctive is its accessibility,” said Cecil ia Décima Oneto, a postdoctoral researcher at The James Hutton Institute who works on gene editing in berries and was not involved in the PubPlant project. “It was designed with usability in mind, so that even researchers without a strong background in bioinformatics can explore the data effectively. The integration of interactive timelines, phylogenetic trees, and direct links to primary publications allows users to move efficiently from raw data to biological interpretation. This reduces duplication of effort, saves valuable time, and encourages more integrative approaches to plant biology.”

How PubPlant Could Revolutionize What We Eat

Having high-quality genomes is not an academic luxury: it is the strategic backbone of 21^st-century agriculture. Modern breeding techniques—such as genomic selection, molecular marker design, or precision gene editing—depend heavily on knowing exactly where the genes of interest are.

Looking back to the 2000s or even the early 2010s, many of today’s advances in breeding—from precision gene editing to identifying genes associated with resistance, nutritional quality, or tolerance to climate stress—would simply not have been possible.

Today, having these detailed Plant Genomic Atlas helps breeders answer key questions—for example, identifying the resistance gene to an emerging disease or the loci behind drought tolerance, determining which variants drive higher vitamin or protein content or trigger allergens, and assessing which edits can be made without sacrificing other desirable traits.

Even the most modern biotechnology techniques—from GMOs to the recent molecular scissors known as CRISPR—cannot unleash their full potential without a “Genomic Atlas” to guide exactly where and how to direct a gene transformation strategy without affecting genes related to other positive traits.

“PubPlant makes it easier to identify published genomes across many plant species at a single site,” added Bolger. “This can speed discovery of useful traits—drought tolerance, pest resistance, nutritional quality—by showing how they are distributed across plants. For breeders, it means faster identification of promising species or varieties; for researchers, it provides a foundation for studying evolution and biodiversity at scale.”

Beyond Commodity Crops

The researchers tested a real-world application of PubPlant by analyzing food crops. Using FAOSTAT data, they examined genome coverage across the plant families with the greatest number of food species. They found that families with the most sequenced genomes—Poaceae, Fabaceae, Solanaceae, Rosaceae, and Brassicaceae—also included many of the world’s most important crops. At the same time, they observed that other groups, such as Apiaceae, Amaryllidaceae, and Grossulariaceae, remain underrepresented, indicating opportunities for future sequencing.

The researchers noted that although all key food crops have already been sequenced, the species that remain unsequenced tend to be important in lower-income countries. For countries where crops like cassava, teff, or indigenous legumes play key roles in nutrition and livelihoods, such maps can be transformative. “PubPlant offers a concise synopsis of the genomic data presented in published papers. For smaller institutes or researchers without access to costly journal subscriptions, this provides an accessible entry point to key information that would otherwise be difficult to obtain,” said Bolger. “Projects working with large-scale clade-level pangenomes will benefit most, as PubPlant helps identify potential candidate genomes. PubPlant also has a visualization which highlights orders and families lacking sequenced genomes, providing valuable guidance for targeting future sequencing efforts,” noted Bolger.

Leveling the Field: How Open Genomic Tools Empower Breeders Worldwide

One of the most valuable aspects of PubPlant is that it democratizes access to cutting-edge genomic information. Public-sector scientists from lower-resourced countries, as well as SMEs and small breeding programs, can use this data to make more informed decisions.

In a global context where food security, climate change, and pressure from agricultural land expansion are constant challenges, open and updated tools like PubPlant can help level the playing field for all actors in the agri-food system.

The pace of plant genomics growth shows no signs of stopping—and for that very reason, PubPlant is not a static repository. It is updated monthly, systematically incorporating new genomes from the literature, and is ready to integrate new data types such as pangenomes, multi-omics analyses, and long-read assemblies.

In future, plant researchers are looking for platforms that integrate with digital agriculture systems, AI-powered breeding programs, or regulatory frameworks that require genetic traceability?⁶ Is PubPlant up to the task?

“Maintaining the existing functionality is already a significant task, so we are careful about adding features that could increase workload substantially. That said, we recently added links to ‘Plants of the World Online’ for all published species, and we will continue to prioritise enhancements that provide high value to users while remaining sustainable to support,” explained Bolger.

The plant genomics revolution is no longer a future promise; it is happening now, the team believes. Looking ahead, Décima Oneto added, “This type of dynamic and openly available resource will be highly valuable across many areas of plant research. It can support the identification of agronomic traits, strengthen breeding programs, and ultimately help develop more resilient crops for a changing climate.”