H2020 Plant.ID Project: Molecular Identification of Plants
- Type Project
- Status Filled
- Execution 2018 -2021
- Assigned Budget 4.062.035,52 €
- Scope Europeo
- Main source of financing H2020
- Project website Proyecto Plant.ID
Accurate and rapid molecular identification approaches are urgently needed to help scientists identify and characterize plants and their products for applications ranging from medicine to the illegal trade of endangered species. Over the past decade, countless advances in genomic data, DNA sequencing, and molecular identification methods have placed many new tools in the hands of scientists to address a variety of applications.
Supported by the Marie Skododowska-Curie Actions program, the Plant.ID project will prepare a new generation of biosystematists to fully exploit the potential of these and other new methods. The team will focus on developing molecular plant identification through species delimitation, metabarcoding, gene capture, and genomic barcoding. Show the project objective.
Massive DNA sequencing data provide new insights into biodiversity at several different scales. At shallow phylogenetic levels, it allows us to discover population-level lineages and, therefore, further develop a phylogenetic model that accounts for population-level phenomena, as well as allele migration between populations.
- In WP1, theoretical and experimental developments in this field were reviewed and further developed and tested by ESR 1 using Arctic Silenus species. Herbarium specimens provide scientists with plant material for phylogenetic studies. ESR 3 used this type of data to assess species delimitation as well as deeper phylogenetic patterns in the hemiparasitic genus Euphrasia. At another level, massive sequencing of DNA collected from soil samples allows scientists to identify taxonomic diversity to accurately assess ecological turnover and gradients at both spatial and temporal scales, to which ESR 2 contributed using plant DNA collected from soil samples. DNA metabarcoding is a research method developed for biodiversity assessment from DNA-containing substrates. It holds great promise for plant identification, but more markers need to be developed for accurate species identification.
- WP2 ESRs have worked on developing and testing new approaches to assessing plant molecular diversity that go beyond amplicon-based sequencing and instead utilize shotgun sequencing, metagenomics, artificial intelligence, and machine learning. These methods enable accurate identification and relative quantification of plant species in substrates, improving the ability to screen, authenticate, and control such substrates, including herbal supplements, food products, pollen traps, soil sediments, water samples, and wood. Genome sequencing data is used in metabarcoding, as it avoids amplification bias and enables quantification of constituents.
- WP3 therefore aimed to develop new genetic and molecular approaches for plant identification. Each project continued to follow up on the work undertaken during the first reporting period and followed up on the objectives planned for the second reporting cycle. To this end, chemical and molecular methods were developed for the historically important medicinal plant, the cinchona tree. Customized target-capture bait panels were developed for the commercially valuable Aloe, leading to the largest dataset produced to date on carbon isotope values of aloes. Target-capture and metagenomic sequencing of commercial salep powder samples from suppliers and online marketplaces was developed to test their composition and provenance. A range of bioinformatics tools were tested against a Begonia population with a known genetic composition to establish workflows for analyzing Begonia from radiations of different species. More and more organizations are routinely applying DNA-based techniques for quality monitoring and assessment. Regarding plant identification, tailored applications for end-users in society are still in their infancy.
- Therefore, all ESR projects in WP4 aimed to develop solutions for presenting research results that were easy for end users to interpret. Thus, wood samples from African hardwoods important in trade were analyzed by ESR12, resulting in new markers to discriminate between those that can be legally traded and those that are. ESR13 developed a new bioinformatics PI (pelinas) to analyze the level of adulteration in medicinal herbs and foods. ESR14 developed methods to understand the historical geography and lineage of important medicinal plants in Africa. ESR15 developed AI methods to analyze traded ebony and identify protected species from those that are. This work has been disseminated through 42 oral and poster presentations and 11 articles in peer-reviewed journals, reaching 6,800 members of the scientific community. Outreach efforts using various forms of dissemination have also resulted in reaching 470,000 members of the general public.
Plants provide food, animal feed, medicines, and building materials. But they also negatively affect us through pollen allergies, poisonous species, invasive species, and as adulterants in medicinal herbs. Yet, plants are the most promising biological resource for our future. The current risks of extinction and declining taxonomic knowledge require accurate and rapid identification approaches to understand and enhance botanical biodiversity. Advances in genomic data and DNA sequencing are revolutionizing plant systematics, and modern molecular identification methods allow for precise plant identification in ways that were technically impossible just a decade ago.
Recently, it has become possible to detect substitution in herbal pharmaceuticals, monitor invasive alien species, track fragments such as pollen and spores, uncover illegal trade in endangered species, perform rapid and accurate assessments of molecular biodiversity, and study historical plant diversity through DNA in museum specimens. However, to efficiently harness the potential opportunities afforded by new genomic techniques, today's society urgently needs trained biosystematists with expertise in both taxonomy and the management of massive amounts of genomic data. Plant.ID has addressed these challenges by bringing together academic and non-academic partners, including regulatory agencies, industry, SMEs, and NGOs, to develop molecular plant identification through customized approaches including species delimitation, metabarcoding, gene capture, and genomic barcoding, in order to empower stakeholders with simplified molecular plant identification.
By combining classical taxonomic expertise with cutting-edge genomic approaches, Plant.ID brought together a network of biodiversity researchers and institutions to address pressing impediments to describing and assessing threatened plant biodiversity; trained a new generation of 15 researchers with immediate relevance to harnessing the central role of plants in the modern world; and built a network for future collaborations within and beyond Plant.ID.
Many of the nearly 400,000 plant species provide food, animal feed, medicines, and building materials. In addition to these positive impacts, plants also negatively affect us through pollen allergies, poisonous species, invasive species, and adulterants in medicinal herbs. However, plants are the most promising biological resource for our future. The current risks of global flora extinction and the sharp decline in taxonomic expertise demand rapid and accurate identification approaches to understand and assess botanical biodiversity. Advances in genomic data and DNA sequencing are revolutionizing plant systematics, and modern molecular identification methods allow for precise plant identification in ways that were technically impossible just a decade ago.
Recently, it has become possible to detect substitutions in herbal pharmaceuticals, monitor invasive alien species, track fragments such as pollen and spores, uncover illegal trade in endangered species, perform rapid and accurate assessments of molecular biodiversity, and study historical plant diversity through DNA in museum specimens. However, to efficiently harness the potential opportunities offered by new genomic techniques, today's society urgently needs trained biosystematists with expertise in both taxonomy and the management of massive amounts of genomic data. Plant.ID will innovatively address these challenges by bringing together academic and non-academic partners, including regulatory agencies, industries, SMEs, and interested NGOs, with the aim of developing molecular plant identification through tailored approaches for species delimitation, metabarcoding, gene capture, and genomic barcoding, in order to empower stakeholders with simplified molecular plant identification. By combining classical taxonomic expertise with cutting-edge genomic approaches, Plant.ID will empower a new generation of ESRs who will have immediate relevance in harnessing the central role of plants in the modern world.
Plants are a crucial resource for our planet, providing food, medicine, and building materials. However, they can also negatively affect us, such as poisonous plants and pollen allergies. Therefore, it's important to be able to identify plants; however, the process isn't always straightforward.
The aim of the EU-funded Plant.ID project, supported by the Marie Skododowska-Curie Actions programme, was to address the challenges of plant identification. Plant.ID, a collaborative network within Europe, brought together academic and non-academic partners to develop novel and scalable methods for DNA-based plant identification. “This may sound like shooting a fly with a cannon, but DNA provides robust and simplified ways to identify plants,” notes Hugo de Boer, project coordinator. The project also supported the career development and training of the next generation of researchers who will develop these cutting-edge solutions for plant identification. “A key motivation of this project for me was to provide a training opportunity for 15 talented young people in this field. The most inspiring and rewarding thing about science is recruiting smart people—often smarter people—and helping them achieve their career development goals,” reflects de Boer. Describing and Assessing Plant Diversity To meet the overall objective, the project was structured into four work packages.
The first focused on the definition of species as taxonomic entities as a basic requirement for identifying species from DNA.
The second and third work packages focused on specific approaches to DNA-based identification. The fourth examined practical applications of DNA-based plant identification. “As a team, the project has advanced the field in several key areas, including molecular pollen identification, plant metagenomics for dietary analysis, phylogenomics of polyploids, plant museomics, and plant diversity assessment from environmental soil DNA,” de Boer confirms. For example, in the first work package, theoretical and experimental developments in massive DNA sequencing were tested using Arctic Silenus species. This work can help provide underlying information for an updated taxonomy of the group.
In work package two, early-stage researchers worked on developing and testing new approaches to assessing plant molecular diversity that go beyond amplicon-based sequencing. "These methods allow for precise identification and relative quantification of plant species in substrates," de Boer adds. They also improve the ability to filter, authenticate, and monitor these substrates.
In Work Package 3, new genetic and molecular approaches for plant identification were developed. In Work Package 4, the goal was to develop solutions for presenting research results that were easy for end users to interpret. More information about the work carried out in the project can be found on the Plant.ID website. What's next for Plant.ID? "The project has brought together a loosely organized group of scientists into a strong collaborative network.
There is still much to be done in the field of molecular plant identification, but the network can build on its achievements by gradually building on the innovative foundation it has established," de Boer reports. The project has identified additional gaps and challenges that are now being explored. "We are looking into expanding our collaboration and applying for Horizon Europe research funding to develop new approaches, as well as working with stakeholders to implement these methods to achieve societal impact," de Boer concludes.
Mobilizing our team of grantees and partners, Plant.ID has been working to translate cutting-edge empirical innovations into applied research and development, with key players in species delimitation, DNA barcoding, and molecular identification. This is allowing us to address previously unaddressable questions in biosystematics. The proposal laid the groundwork for a project that would advance beyond the state of the art, but more importantly, it also envisioned the consortium initiating new synergistic collaborations through the ESR projects. This openness to innovation is key for projects seeking to capitalize on scientific developments that occur after proposal submission or during project initiation and early implementation.
At the midpoint, we can clearly see that all projects are specific, measurable, achievable, relevant, and time-bound, and our ESRs are working on specific deliverables relevant to the project and their PhDs. Furthermore, many ESRs have adopted and incorporated cutting-edge developments into their projects to increase the scientific and societal relevance of Plant.ID. Furthermore, several collaborations between ESRs, as well as between projects, are underway to help Plant.ID achieve its vision beyond cutting-edge synergies.
- UNIVERSITETET I OSLO (UNIVERSITY OF OSLO)
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