Every six years, the botanical community convenes for what has been called their “Olympic Games”: the International Botanical Congress. This year, the XXth congress brought over 3 000 attendees from all parts of the world from 21st to 27th July to sunny Madrid – during a major heatwave. Among them were several ERGA members, aiming to make contact among each other and to get more botanists involved in our initiative. Additionally, this was a great opportunity to exchange with other large-scale sequencing projects targeting plants, such as GAP (Genomics for Australian Plants), 10KP (Ten Thousand Plant Genomes) and DToL (Darwin Tree of Life), putting ERGA on the map as the only cross-borders and community-driven initiative among them.
Katja inviting all IBC attendees to the ERGA satellite meeting at the end of her talk, which highlighted the importance of common standards and reproducibility in large-scale reference genome production. (Photo: Sophie Maiwald)
Already on Tuesday evening, the symposium “Large-scale Generation and Utilisation of Reference-Quality Genomes from Plants”, organised by Peter Hollingsworth (Royal Botanic Garden Edinburgh) and Sean Graham (University of British Columbia), and the ensuing workshop of the 10KP project sparked heated discussions. These ranged from fair attribution and involvement of sample providers and other experts, open data access and findable vouchers, capacity building and “helicopter” science, i.e. the study of a country’s biodiversity without involving any local researchers, to the inequality of opportunities among the global North and South, which is further exacerbated by current technological limits such as the necessity of liquid nitrogen freezing. Specifically with respect to ERGA, several participants asked how they could contribute community genomes.
The new ERGA badges served their purpose well and the ERGA satellite meeting was announced in all central places. (Photos: Katja Reichel)
Although the meteorological conditions and a wave of COVID infections had somewhat diminished the field, over 20 attendees currently based e.g. in Spain, Portugal, France, Great Britain, Germany, Austria, Italy and Hungary – plus guests from China and Australia – also came to the ERGA plant specialists’ IBC satellite meeting on Wednesday afternoon. There, Katja Reichel gave an introduction to ERGA and to several current endeavours craving input from the plant community, such as the rogue genomes working group and plant sampling SOP. About half of the group then stayed on to network and discuss general issues during plant reference genome production. This included topics as diverse as the lack of funding opportunities for big genomes (such as present in many plants), the missing overview of the species whose genomes are currently being sequenced (and by whom / prioritisation), the lack of software adapted e.g. to genomes of uneven ploidy or including huge repeat clusters which defy even long-read sequencing, the challenges of genome annotation, problems with high molecular weight (HMW) DNA extraction, as well as the isolation of plant genome scientists even within ERGA. However, the meeting also brought forth the expertise which already exists on some of these issues, and highlighted the need to connect and join forces. You can find the slides presented by Katja here.
Both from the meeting and from further conference break discussions arose several ideas for action. These include a more proactive, transparent communication on the aims and “rules” of ERGA within the (plant) science community and also towards partner projects such as DToL, the registration of ongoing reference genome sequencing projects, including community genomes, e.g. through GoaT, the establishment of a reporting standard for both successful and failed HMW DNA extractions alike, and a dedicated keybase channel for, as well as regular online / hybrid meetings of, the ERGA plant specialist community.
Hoping that these ideas will gradually be implemented, we thank Luisa Marins, Chiara Bortoluzzi and Christian de Guttry for help with the organisation and advertisement for the satellite meeting, all participants and discussion partners for their contributions, as well as the IBC organisers for giving us this opportunity to connect.
About the Author
Katja Reichel is co-chair of the Sampling and Sample Processing Committee and regularly speaks out for plants within the ERGA community. At the IBC, she presented a bioinformatic pipeline for the standardised generation of annotated plastid genomes from Illumina short reads. Her research on population and conservation genomics of partially clonal plants currently focuses on Arnica montana and is partially financed by the Biodiversity Genomics Europe project.
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