Global Genome Biodiversity Network Research Articles

Luomus’ Genomic Resources Collection Available as Open Data Through FinBIF

There is an increasing demand for high-quality genetic samples for biodiversity research as the techniques are rapidly developing and the costs are decreasing. The Finnish Museum of Natural History Luomus, an independent research institute within the University of Helsinki holding and developing the national natural history collections, has joined the Global Genome Biodiversity Network (GGBN; http://www.ggbn.org/ggbn_portal/) and established a Genomic Resources Collection (GRC) in 2018. In March 2019, the Luomus GRC comprised 2500 DNA extractions and 4000 vertebrate tissue samples amassed in approximately the last 10 years. The DNA extractions are mainly of lichens, polypores, beetles, flies, molluscs and crustaceans of worldwide origin, reflecting the focal organism groups of research groups in Luomus. The deep-frozen tissue samples are mostly of Finnish birds and mammals, as accessions of vertebrate specimens acquired to Luomus’ collections are sampled. High-quality whole-genome DNA extracts will also be prepared. We expect the GRC to increase rapidly in numbers of samples within the coming years. Furthermore, the collection will also serve the many active research groups in the Faculty of Biological and Environmental Sciences of the University of Helsinki. The GRC collection follows the best practices of the Global Genome Biodiversity Network (GGBN) concerning long-term storage and physical quality of samples, and international agreements (the Convention on Biological Diversity, the Nagoya Protocol, CITES) as regards the legitimacy of the samples. The GRC samples are always cross-linked with the taxonomically identified and georeferenced voucher specimen from which it is separated. Each GRC sample gets a Unique Resource Identifier HTTP-URI, which is a derivative of the unique specimen ID used in Luomus’ Collection Management System (CMS) ‘Kotka’. The sample tubes are cryolabelled with the QR code on the lid of the tube. The voucher specimens are deposited in Luomus’ collections or in another international public repository. The data on the GRC samples form part of the Open Data distributed through the Finnish Biodiversity Information Facility FinBIF species.fi (Data policy: https://laji.fi/en/about/960), and will be made searchable at the web portal in 2019. The specific database functions to meet the needs of Luomus’ GRC are developed by Luomus’ Biodiversity Informatics Unit and implemented in Kotka. We have already implemented part of the database tools to manage the compliance with the Nagoya protocol. The tool for registering material transactions (donations / loans) makes use of the Application Programming Interface (API) provided by the Access and Benefit Sharing Clearing House (ABS-CH) and includes links to the ABS-CH webpage (https://absch.cbd.int/). The ABS-CH shows the contact person or organization details of the provider country, and the country-specific requirements for access to genetic resources, when present. The necessary information and documentation (letter of Prior Informed Consent, Mutually Agreed Terms, Material Transaction Agreement, and other permits) are linked from the material transactions to the relevant specimens.

Management and GGBN publishing of tissue and DNA extract data through Specify software

Due to the recent establishment of the Global Genome Biodiversity Network (GGBN) data portal, we have extended Specify collections management software (http://www.sustain.specifysoftware.org/) to more effectively manage, publish, and integrate tissue and DNA extract data by adding support for the GGBN data schema. Specify’s database design now includes a number of data fields and tables proscribed in GGBN standard vocabularies. We also realigned some of the underlying table relationships to address the needs of specimen curation and collection transactions for extract and tissue samples. Specify now also supports “Next Generation” sequencing metadata with fields to record NCBI SRA ID numbers for web-linking tissue and extract metadata to entries in the NCBI SRA databases. With the ongoing evolution of the TDWG Darwin Core (DwC) standard for specimen data exchange, we generalized Specify 7’s data publishing capabilities to export collections data to any DwC or other standards-based, exchange schema. This generic, external schema mapping capability enables Specify collections to design and map data packages to integrate their data with any community aggregator or collaborative project database based on Darwin Core or other community standard-based format. The development of these versatile new integration capabilities was in collaboration with, and through financial support from GGBN. This talk will highlight these changes in the context of delivery of museum tissue and extract data records to the GGBN data portal for aggregation.

Global Genome Biodiversity Network – Infrastructure for genomic research

Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards. In response to these challenges, natural history museums, culture collections, herbaria, botanical gardens and others have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry of relevant institutions, it is difficult and time-consuming to locate the needed samples. The Global Genome Biodiversity Network (GGBN) was created to fill this gap by establishing a central access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions (e.g. the Nagoya Protocol). The GGBN is rapidly growing and currently has 70 members and works closely together with GBIF, SPNHC, CETAF, INSDC, BOLD, ESBB, ISBER, GSC and others to reach its goals. Knowledge of biodiversity biobank content is urgently needed to enable concerted efforts and strategies in collecting and sampling new material and making ABS a reality. GGBN provides an infrastructure for making genomic samples discoverable and accessible. While respecting national law, GGBN requires that its members comply with the provisions of the Nagoya-protocol. Thus researchers, collection-holding institutions, and networks should adopt a common Best Practice approach to manage ABS, as has been developed by GGBN. A Code of Conduct; recommendations for implementing the Code of Conduct (the Best Practices), and implementation tools, such as standard Material Transfer Agreements (MTA) and mandatory and recommended data fields in collection databases, are tools which will aid compliance. This talk provides an overview of GGBN and comprises updates on GGBN’s best practices on ABS and the Nagoya Protocol, with examples of their use and applicability.

Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution.

The Global Genome Initiative has sequenced and released 1961 DNA barcodes for genetic samples obtained as part of the Global Genome Initiative for Gardens Program. The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life. The genetic samples were deposited in the Smithsonian Institution’s National Museum of Natural History Biorepository and their records were made public through the Global Genome Biodiversity Network’s portal. The DNA barcodes are now available on GenBank.

Environmental samples, eDNA and HTS libraries – data standard proposals from the Global Genome Biodiversity Network (GGBN)

Environmental samples, eDNA and HTS libraries – data standard proposals from the Global Genome Biodiversity Network (GGBN)

The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing.

ABSTRACTThe U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD). The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol.

Explanation of the Nagoya Protocol on Access and Benefit Sharing and its implication for microbiology.

Working with genetic resources and associated data requires greater attention since the Nagoya Protocol on Access and Benefit Sharing (ABS) came into force in October 2014. Biologists must ensure that they have legal clarity in how they can and cannot use the genetic resources on which they carry out research. Not only must they work within the spirit in the Convention on Biological Diversity (https://www.cbd.int/convention/articles/default.shtml?a=cbd-02) but also they may have regulatory requirements to meet. Although the Nagoya Protocol was negotiated and agreed globally, it is the responsibility of each country that ratifies it to introduce their individual implementing procedures and practices. Many countries in Europe, such as the UK, have chosen not to put access controls in place at this time, but others already have laws enacted providing ABS measures under the Convention on Biological Diversity or specifically to implement the Nagoya Protocol. Access legislation is in place in many countries and information on this can be found at the ABS Clearing House (https://absch.cbd.int/). For example, Brazil, although not a Party to the Nagoya Protocol at the time of writing, has Law 13.123 which entered into force on 17 November 2015, regulated by Decree 8.772 which was published on 11 May 2016. In this case, export of Brazilian genetic resources is not allowed unless the collector is registered in the National System for Genetic Heritage and Associated Traditional Knowledge Management (SisGen). The process entails that a foreign scientist must first of all be registered working with someone in Brazil and have authorization to collect. The enactment of European Union Regulation po. 511/2014 implements Nagoya Protocol elements that govern compliance measures for users and offers the opportunity to demonstrate due diligence in sourcing their organisms by selecting from holdings of 'registered collections'. The UK has introduced a Statutory Instrument that puts in place enforcement measures within the UK to implement this European Union Regulation; this is regulated by Regulatory Delivery, Department for Business, Energy and Industrial Strategies. Scientific communities, including the private sector, individual institutions and organizations, have begun to design policy and best practices for compliance. Microbiologists and culture collections alike need to be aware of the legislation of the source country of the materials they use and put in place best practices for compliance; such best practice has been drafted by the Microbial Resource Research Infrastructure, and other research communities such as the Consortium of European Taxonomic Facilities, the Global Genome Biodiversity Network and the International Organisation for Biological Control have published best practice and/or codes of conduct to ensure legitimate exchange and use of genetic resources.

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA.

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall “genome-quality” DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA “greater than X kb” as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (“DNA Threshold” and “Percent above Threshold”) introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.

Global Genome Biodiversity Network: saving a blueprint of the Tree of Life - a botanical perspective.

Background Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples.Scope The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on ‘harvesting’ the Tree of Life for vascular plant taxa to enable genome-level studies.Conclusion While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera.

The Global Genome Biodiversity Network (GGBN) Data Standard specification.

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard

The importance of biobanking in molecular taxonomy, with proposed definitions for vouchers in a molecular context

The importance of biobanking in molecular taxonomy, with proposed definitions for vouchers in a molecular context

The Global Genome Biodiversity Network (GGBN) Data Portal

The Global Genome Biodiversity Network (GGBN) was formed in 2011 with the principal aim of making high-quality well-documented and vouchered collections that store DNA or tissue samples of biodiversity, discoverable for research through a networked community of biodiversity repositories. This is achieved through the GGBN Data Portal (http://data.ggbn.org), which links globally distributed databases and bridges the gap between biodiversity repositories, sequence databases and research results. Advances in DNA extraction techniques combined with next-generation sequencing technologies provide new tools for genome sequencing. Many ambitious genome sequencing projects with the potential to revolutionize biodiversity research consider access to adequate samples to be a major bottleneck in their workflow. This is linked not only to accelerating biodiversity loss and demands to improve conservation efforts but also to a lack of standardized methods for providing access to genomic samples. Biodiversity biobank-holding institutions urgently need to set a standard of collaboration towards excellence in collections stewardship, information access and sharing and responsible and ethical use of such collections. GGBN meets these needs by enabling and supporting accessibility and the efficient coordinated expansion of biodiversity biobanks worldwide.