Genetic resources are a core biological resource. Obtaining clear genetic information can be of great significance for human health, society and economic development. The Earth BioGenome Project (EBP) aims to sequence, catalog and characterize the genomes of all eukaryotic organisms on Earth over a 10-year period.
The EBP is currently one of the largest life science research projects in the world. Through it we will have a deeper understanding of the organisms that exist widely on the earth from the perspective of their genetic information, and this will enable us to protect global biodiversity.
The EBP project was launched three years ago, and while going through many difficulties has achieved fruitful results. BGI-Research is an important participant in the project and its research has been published in international authoritative journals. In January, the "Proceedings of the National Academy of Sciences" (PNAS) released a special EBP update, which included two articles participated by BGI-Research. SEQ.cn invited Liu Xin, senior vice president of BGI-Research to share the current progress of the EBP project and its future development direction.
The Early Stages
The EBP plan was launched in 2018 and is divided into three stages. The first two years (2018-2020) were the project start-up stage, and the first stage of the project started from the end of 2020. The past year was the start year of the project and was also a year of important progress.
An important first achievement of the EBP project has been to establish global international standards to define the project. Liu Xin noted that the proposal of the project originated from the Biodiversity Conference held in the United States in 2018. Yang Huanming, Xu Xun, Zhang Guojie and others put forward the concept of a global biological genome for the first time.
In November of the same year, a kick-off meeting held in London laid the foundation for the implementation of the project. The meeting determined the goals of the EBP project, clarified the project direction, established the project secretariat, and formed a sub-project system.
In the first few years of the project, the international centers involved in the project also worked out detailed sub-project plans to meet the goals. Currently, the EBP project team has improved the overall organization and management system, established international exchange organizations including sample collection centers, genomic technology centers, affiliated special program centers, etc., and formulated a number of standards and specifications, covering project participation, data sharing, intellectual property acquisition and sharing, etc.
EBP now has confirmed participation by 43 institutions, with 44 affiliated projects from 21 countries on all continents except Antarctica. This demonstrates the true global nature of this undertaking.
Some of the sub-projects sequencing different species have already produced data. Currently, the projects have contributed 1,719 eukaryotic genomes. Among them, 316 have met the "reference genome" standard of EBP and reached the level of "reference genome".
Challenges are not insurmountable
Three years after the EBP project was launched, important progress has been made, but it has also faced many challenges.
The first difficulty of the project was the acquisition, identification and preservation of millions of eukaryotic specimens. Some specimens could be obtained from existing samples from the Global Genome Biodiversity Network (GGBN) , however, a permitting process of weeks or even months was still required due to different national policies. In order to obtain better DNA quality, some species still needed fresh biological samples to complete the analysis, which needs to overcome the multiple difficulties from regions and environments, and a fast and effective way of sample preservation is very important. If necessary, the extraction was started at the nearest laboratory and then the tests were carried out in stages. At the same time, newly collected samples needed to undergo strict species identification to ensure the accuracy of subsequent results.
Ensuring the acquisition of high-quality genomes has also been difficult. The genome research basis of different species is quite different, and the genome complexity of different eukaryotes is different, so it is difficult to unify the standards. For example, compared with the human genome, which has been researched for more than 20 years, many eukaryotes still lack reference genomes and require de novo sequencing and assembly, which poses huge challenges to both sequencing technology and bioinformatics analysis.
Compared with vertebrates, about 70% of flowering plants have no genetic data, let alone complete genome information. Plant genomes vary greatly in size and are not uniform in the number of chromosomes occurring in the nucleus of a cell, all of which pose challenges for later genome assembly. Therefore, notes Liu Xin: "When analyzing the genomes of different organisms, we need to pay special attention to the quality of genome assembly, initiate personalized analysis, and avoid the possible impact of genome assembly results on subsequent scientific discoveries."
The ups and downs of the EBP project lie in the project itself, and also in a variety of unforeseen difficulties waiting to be overcome. Yet there is still tremendous enthusiasm. The success of the early Human Genome Project, as well as in vertebrates (10,000 Vertebrate Genomes Project, G10K), birds (10,000 Avian Genomes Project, B10K), marine invertebrates and plants (1000 Plants Project, 1KP) has provided valuable experience for the development of the EBP project. At the same time, the improvement of sequencing technology has also laid a solid technical foundation for the successful completion of the project.
“In our day-to-day scientific research, we cultivate the determination to break through difficulties and an enthusiasm for research. What we pursue are not short-term results, but higher research goals in three or five years, or even decades. In the EBP project, the multi-center international cooperation provides an academic discussion platform for researchers from all over the world and expands their ability to solve problems. At the same time, the proposal of solutions to the core problems motivates us to move forward," said Liu Xin.
Connecting All Lives, Benefiting Us Today
The EBP project looks to the future but has already demonstrated excellent results. At the same time it has also shown practical significance for society today.
Since the outbreak of COVID-19, more and more people have begun to pay attention to the concept of "one health" - as a community with a shared future, all organisms are interdependent, and one organism may affect the health of another organism in parasitic or other forms. health status. The EBP project aims to understand the genetic information of all eukaryotic organisms that are directly and indirectly related to us, so that we can understand the entire ecology from a systematic perspective, allowing us to not only focus on "me" - human beings, but also more about the "surroundings" – ecology.
In the prevention and control of COVID-19, gene sequencing helps us to better identify the virus and its potential hosts and assist in tracing the source. The latest article published in PNAS also highlights the role of the EBP project in "one health". Through the EBP project, a DNA sequence library of all known eukaryotes can be created, biological correlations can be predicted, and it will also assist us in effective prevention of biodiversity loss and pathogen spread and enable us to continuously monitor and protect our ecosystems.
The Power of International Cooperation
International cooperation plays a critical role in the initiation and implementation of the EBP project.
EBP allows the affiliated projects to raise funds on their own. Each international center fully mobilizes resources to overcome difficulties, complete funding preparations and deliver results, with supports and instructions from EBP.
At the beginning of the project, the key centers reached a cooperation intention, broke through the barriers of international cooperation, reached a consensus on "openness, cooperation, and sharing", formulated standards and norms, and moved forward. In the process of project implementation, all centers have fully cooperated in overcoming geographical distance through online communication during the pandemic, enthusiastic academic discussions during difficult times, and celebrating together online after solving difficulties. The high level of coordination among these projects will create synergies in biodiversity research and social outcomes, benefiting both human and ecological development for years to come.
The China Research Center, represented by BGI-Research, has undertaken several sub-projects in the EBP, achieving fruitful results. In 2021 alone BGI-Research has completed the genome sequencing and assembly of more than 1,000 species, and published them in authoritative academic journals such as Nature, Nature Communications, PNAS, Molecular Plant, and Science Bulletin.
In the context of a community with a shared future for one health approach, the Earth BioGenome Project will open the door for mankind to understand and protect ecology. At the same time, Liu Xin says: "I hope that more aspiring and capable centers will join the Earth BioGenome Project, helping is to complete the EBP project faster and more fully, providing more genomic information for a full understanding of biological ecology, and helping human beings and ecology co-exist harmoniously”.