Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

Question

1. What is the role of the ERGA Sampling and Sample Processing committee (SSP)?

2. What are the initial responsibilities of the Sampling and Sample Processing committee (SSP) in ERGA?

3. What is the significance of revisiting biodiversity genomic metadata standards?

4. What is the purpose of the ERGA manifest?

Accepted Answer

The ERGA Sampling and Sample Processing committee (SSP) aims to aid participating researchers by establishing standards for sample/specimen metadata, prioritizing species for genome sequencing, and developing taxon-specific collection guidelines. SSP serves as the sample provider's entry point to the ERGA genomic resource production infrastructure, ensuring high-quality standards are upheld throughout sample collection and processing. The committee's efforts contribute to the development of standardized operational procedures and sample provider support, incorporating the FAIR and CARE principles, species prioritization, and workflow development. This information is valuable for individuals and other initiatives in the field of genomics resources.

Accepted Answer

The initial responsibilities of the Sampling and Sample Processing committee (SSP) in ERGA include establishing standards and mechanisms to collect sample/specimen metadata, prioritizing species collection, and developing taxon-specific collection guidelines for the biological material underlying ERGA's mission. The SSP serves as the sample provider's entry point into ERGA's distributed genomic infrastructure and helps ensure standardized sample processing. As ERGA evolved, additional tasks emerged, such as providing guidance to sample providers for legal compliance and facilitating sample shipping between providers and sequencing centers. The SSP's efforts contribute to the success of ERGA's mission to create a publicly available reference genome catalogue for all European eukaryotic biodiversity.

Accepted Answer

Revisiting biodiversity genomic metadata standards is crucial to ensure they are scientifically comprehensive and align with current ethical, legal, and social standards for data governance. This is particularly important as the demand for freshly collected, wild specimens increases with the rise of initiatives working towards complete reference genomes for all eukaryotic life. By revisiting these standards, we can ensure that they are inclusive and recognize the rights of Indigenous Peoples, aligning with the CARE principles of Indigenous data governance. This also complements the FAIR principles, promoting responsible and open data sharing in the field of genomics.

Accepted Answer

The ERGA manifest aims to collect standardized, high-quality metadata that remains linked to the genome across relevant repositories. It supports ERGA's goal to ensure consistency and excellence in metadata collection. The manifest includes detailed information such as sample identifiers, taxonomic details, sample type, sequencing partner, sample collection event, taxonomic identification and uncertainty, DNA barcoding, biobanking and vouchering, regulatory compliances, and other relevant comments. Upon validation, mandatory metadata fields are brokered to the European Nucleotide Archive (ENA) under a dedicated BioSample entry, connecting digital sequence data to standardized sample metadata. The ERGA manifest is developed to mitigate the risk of missing information and allows for bi-annual updates to fix accidental exclusions and ensure timely implementation and testing.

Accepted Answer

83% of responding initiatives have a standardized metadata collection procedure in place. This indicates that the majority of biodiversity initiatives prioritize the implementation of a consistent approach to metadata collection. Having a standardized procedure ensures that data collected from various projects can be easily compared and analyzed, leading to more accurate and reliable research outcomes. It also facilitates interoperability between different initiatives, allowing for better collaboration and knowledge sharing within the biodiversity genomics community. The presence of an associated Standard Operating Procedure (SOP) further supports and guides researchers in the metadata submission process, ensuring that the collected data meets the required standards and quality. Overall, the high percentage of initiatives with standardized metadata collection procedures demonstrates the commitment of the biodiversity genomics community to maintaining data integrity and promoting effective data management practices.

Accepted Answer

The ERGA Code of Conduct aims to establish best practices for ethical and legal sample collection. It outlines expectations for permitting at local, regional, national, and international levels, and provides guidelines for minimizing harm during sample collection. The code ensures that researchers adhere to legal and ethical standards, and it includes metadata fields related to regulation and permit requirements for each sample. By requiring the mandatory upload of permits during the manifest submission process, the ERGA Code of Conduct promotes transparency and accountability in legal compliance for sample collection.

Accepted Answer

Vouchering is critical for genomics because it provides a permanent, verifiable, and accessioned record of the identity of the organism being sequenced and, in some cases, a sample of its genetic material (biobanking). It ensures the accuracy and reliability of the sequencing data generated, allowing for future re-examination and updates in case of taxonomic revisions. Vouchers also improve data quality assurance, reduce the risk of data corruption, and eliminate confusion when taxonomic changes occur. Additionally, physical vouchers can be used for various analyses, including photographic, x-ray, CT imaging, and chemical analyses. Biobanked samples offer opportunities for future exploration, such as RNA and secondary genetic marker analyses.

Accepted Answer

Sample transfer involves biological, logistic, and legal issues. Biological challenges include preserving the integrity of nucleic acids through coldchain shipment. Logistic challenges involve accessing appropriate courier services in remote locations. Legal challenges encompass chain of custody forms, material transfer agreements, import/export permits, health certificates, and CITES permits. The ERGA Pilot project highlighted the complexity of these challenges and the need for standard operating procedures (SOPs) to facilitate sample transfer from collectors to sequencing centres.

Accepted Answer

Taxon-specific best-practice guidelines are crucial for large genome initiatives like ERGA to ensure efficient and effective sampling. These guidelines aim to minimize sample collection, maximize data quality, and enhance the scientific utility of the samples. By providing comprehensive yet specific guidelines, the SSP balances the need for detailed information without overwhelming field biologists. Separate working groups focus on different taxonomic groups to create tailored protocols, ensuring consistency and readability. The guidelines will be published on protocols.io, and the challenge lies in involving experts and promoting adoption within the biodiversity community. Integrating, documenting, and distributing this knowledge is fundamental to ERGA and the EBP.

Accepted Answer

Systematic biases in biodiversity genomics affect the accuracy and completeness of data produced, limiting the meaningfulness of conclusions. Biases come in various forms, impacting the human dimension, country representation, and taxonomic breadth. Unbalanced representation of genomes across the tree of life leads to over-representation of certain taxa. Non-model organisms and challenging samples remain underinvestigated due to lack of standardized protocols. Taxonomic expertise disparities exist, with some groups being more abundant than others. Sample bias can occur when samples do not represent the taxon's heterogeneity, while habitat bias under-represents certain habitats. Historical bias may not reflect current diversity. The SSP aims to address these biases by promoting inclusivity, taxonomic representation, and capacity building in understudied regions.

Accepted Answer

ERGA's prioritisation efforts, including the ERGA metadata manifest and stewardship of legal, FAIR, and CARE information, can be utilised, improved, or adopted by other biodiversity genomics projects. These efforts can enhance collaboration and alignment with preexisting biodiversity consortia, such as DToL. The EU-funded project BGE, for example, has utilized ERGA's initial phase to establish key procedures for sampling and sample processing. By uniting ERGA with the DNA barcoding community (BIOSCAN Europe), BGE aims to promote the use of genomics in studying and monitoring biodiversity, creating tools to tackle its decline. BGE will also formalize coordinated efforts, infrastructures, and workflows to generate reference genomes of European species, positioning ERGA as the European node of the Earth Biogenome Project.

Accepted Answer

Species prioritisation can be improved by reflecting on biases, establishing dedicated projects like BGE, and including governing principles in the selection process. This approach aims to approximate governing principles, reduce dependency on circumstantial feasibility and funding availability, and automate the species selection process. By building on the experiences of ERGA and implementing a fully automated process in BGE, species prioritisation can become more balanced and strategic.

Accepted Answer

The challenges in capturing comprehensive metadata for marine samples include the inability of the first version of the metadata manifest to capture sampling depth and only allowing inputting a precise location. This limitation hindered the correct representation of samples from trawls or transects. To address these gaps, updated releases of the manifest now include fields for depth and latitudinal and longitudinal coordinates for two points instead of one for sampling transects, as well as an extended vocabulary for sampled tissues. As genomics advances and more data can be extracted from varying quality samples, extending high ERGA standards to any sample collected for genetic analyses becomes necessary. The increase in frozen archives supported by ERGA will serve as a valuable resource for genome initiatives.

Accepted Answer

Streamlining legal compliance procedures can significantly enhance the efficiency of reference genome generation by ensuring a harmonized approach across different national, political, and cultural borders. By respecting varying legal systems and establishing a unified infrastructure, organizations like ERGA can facilitate cross-country communication and efficient information flow to local authorities. This process helps in identifying and adhering to specific legal requirements for sampling, thereby reducing delays and bottlenecks. Ultimately, a streamlined legal compliance process enables a smoother and more effective reference genome generation pipeline, leading to faster and more accurate results in biodiversity research.

Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

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Most frequently asked questions

1. What is the role of the ERGA Sampling and Sample Processing committee (SSP)?

2. What are the initial responsibilities of the Sampling and Sample Processing committee (SSP) in ERGA?

3. What is the significance of revisiting biodiversity genomic metadata standards?

4. What is the purpose of the ERGA manifest?

5. What percentage of biodiversity initiatives have a standardized metadata collection procedure?

6. What is the purpose of the ERGA Code of Conduct?

7. Why is vouchering critical for genomics?

8. What challenges arise in sample transfer?

9. Why are taxon-specific best-practice guidelines important?

10. What are the impacts of systematic biases in biodiversity genomics?

11. How can ERGA's prioritisation efforts benefit other biodiversity genomics projects?

12. How can species prioritisation be improved?

13. What are the challenges in capturing comprehensive metadata for marine samples?

14. How can streamlining legal compliance procedures improve reference genome generation efficiency?

Citations

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Building a Portuguese Coalition for Biodiversity Genomics

Best practices for genetic and genomic data archiving.

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion

The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

References

The era of reference genomes in conservation genomics.

The Earth BioGenome Project 2020: Starting the clock

The taxonomic impediment: a shortage of taxonomists, not the lack of technical approaches

Operationalizing the CARE and FAIR Principles for Indigenous data futures.

How genomics can help biodiversity conservation.

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