Biocode 2.0 Project

PIs as authors

Introduction (Background/Context/Problem/Scientific Rationale, 250 words)

Biocode 2.0 Moorea Coral Reef Hologenome Sequencing project (the Project) will advance scientific understanding of the unseen biodiversity of reefs and how this diversity responds to and recovers from disturbances. The Project outcomes will help identify how human communities can alter reef health trajectories toward desirable outcomes in the face of global climate change. The Project will create new, diverse, and contextualized marine genomic resources for ecologically, culturally, and economically important organisms and their symbionts from the island of Moorea.

The Project will combine with a data trust model (iPlaces) to better operationalize the FAIR and CARE data principles, including ethical, legal and social issues. Additionally, the Ethnocode Framework will support educational programs through the Atitia Community Center, including “Island Sampling Days’' as nuclei for a range of outreach activities engaging local schools, institutions of higher education, and professional training.

Project Goals (objectives) (250 words)

The primary objective of this project is to:

Methods (250 words)

• Removal of organisms or materials from the reserve.

• Transfer of animals, plants, and/or micro-organisms from outside the reserve to within the reserve, or between different parts of the reserve

• Study or manipulation of non-native species or does your project involve the transfer of animals, plants, and/or microorganisms from outside the reserve to within the reserve, or between different parts of the reserve

Selection of the target species, as well as how and where they are sampled, will be determined through an inclusive co-design process with local community members (across science, education, and culture; civil society and government) at a kick-off workshop on Moorea in March 2024. This workshop will include a focus on how the Project can showcase and extend best practices in Indigenous genomics and data sovereignty (e.g., operationalizing FAIR and CARE principles through socio-technological platforms like iPlaces/GEOME), as well as to engage local stakeholders (scientists, conservation practitioners, decision makers, cultural groups, educators, economic/blue economy actors) in co-design of key project elements, such as the selection of target species and sampling sites, communication channels, and governance choices for the community resources that the Project will develop.

We propose the following draft experimental design for the hologenome database; specific taxa within each of three functional groups will be identified based on community input. We envision collecting hologenome sequencing representatives from the following groups of Moorean marine organisms:

● 10 marine vertebrates, such as: teleost fish species, including culturally significant species like eels (Pā’aihere, I’ihi’, Atoti, Ume tàrei, Pa’ati ha’avare) and if possible elasmobranchs (Ma’o arava, Fai manu) and marine turtles (Honu). Elasmobranchs and turtles would be sampled non-invasively (e.g., swabs and fecal collections) and without harming the animal.

● 10 marine invertebrates, such as: maxima clam (Pahua), black pearl oyster, iconic cnidarians like corals (Pukakana) and large anemones (Pa’i Pa’i), the crown of thorn sea star (Taramea), sponges, tupa and trapezia crabs.

● 10 marine algae and angiosperms, such as: turbinaria, sargassum, lobophora, halimeda, cyanobacterial mats, and seagrass.

This draft design would result in a maximum of 30 target hosts for inclusion in the hologenome database. We will work with Moorea communities to determine the sampling strategy, aiming to have a diversity of samples from around the island and across seasons. To develop an island wide resource, we propose to collect 36 samples (replicates) for each target species over 2 seasons (wet and dry). While we only plan on deep sequencing a single representative for initial hologenome analysis in Year 1, replicates will be added in subsequent years to assess population-level variation in hologenome symbionts, and to explore trophic and other relationships (i.e., interactome mapping) via metabarcoding studies leveraging the ultra-barcoded reef. Initial suggestions will be presented to the community as a starting point for populating the draft experimental design with target taxa.

Community Engagement (250)

Outreach Activities (250)

Project Expected Results (250 words)

Expected Outputs & Management Plan (250 words?)

Expected outputs:

• Genomic and Transcriptomic Data: Ature genetic expression (RNA seq dataset), phylogenetics and phylogenomics (DNA seq dataset) from ~200 sites across the Moorea lagoon.

• Microbial Composition: Ature bacterial (16S rRNA seq dataset) and viral community (RNA seq dataset) composition. Bacterial whole genome assemblies and functional annotation.

• Environmental Metadata: Environmental measurements (e.g., land use, nutrient inputs, salinity) from ~200 sites across the Moorea lagoon.

• Guidelines for co-production

Data management plan:

Genetic sequences will be archived in NCBI, with field and sampling metadata managed in GEOME. iPlaces will host project metadata, and Local Contexts labels will ensure acknowledgment of Indigenous interests and cultural considerations.

What are the societal benefits this project contributes? (economics, education, conservation, distinguish between local and global) (250 words)

Firstly, this project takes a co-produced approach that involves local communities in designing and implementing research. It acknowledges the cultural significance of ature within Polynesian culture and fosters connections between traditional knowledge and scientific research. Additionally, the co-production approach taken in this project is expected to serve as an example of ethically produced research for future studies conducted at the Gump Station. Secondly, the results of this study are expected to inform local management and policies. Ature phylogenies can provide guidance for management plans by highlighting which areas should be protected to maximize genetic diversity. Variation in gene expression and microbiome composition due to environmental factors can also provide guidance for land based conservation plans. Lastly, by engaging diverse audiences through educational programs, internships, and public dissemination of research findings, this project will build local capacity for environmental management and inspire future generations to contribute to conservation efforts.