Submit Data

Goal

The goal of this project is to make seascape genomic data and associated metadata FAIR (findable, accessible, interoperable, and reusable). To maintain interoperability, we require all samples to use short-read sequencing technology, the same bioinformatics pipeline, and the same metadata format.

Seascape genomics is the study of how spatial and environmental factors, such as ocean currents, barriers, and environmental gradients shape the genetic makeup and adaptation of marine species (Riginos et al 2016). Thus, seascape genomic data consists of population genomic data from wild samples, geospatial sampling locations, the date of sampling, and variables that describe the environmental context.

Data requirements

• Samples collected directly from the wild
• Short-read whole genome sequencing (Illumina or AVITI)
  • High coverage data with 12x minimum coverage per individual. 15x is better.
    • Why 12x? This read depth is sufficient for calling heterozygous sites.. Experts have advised us that the heterozygote dropout rate starts to rise below this threshold.
  • Pool-seq data accepted for species with large genomes or that are hard to sample and sequencing individually (like plankton). Minimum requirements are 40 individuals per pool with at least 80x coverage per pool for diploids.
  • For individuals with large genomes (>3Gb), Exome capture data is acceptable
  • Low-coverage data (<12x coverage per individual) not accepted, apply to sequencing grant for deeper coverage
• Multiple individuals.
  • For high coverage data: We aim to have at least 50 individuals per species, but datasets of ~100 individuals spanning a phenotypic or environmental gradient, or that are representative of the species range or population structure would be more ideal. We will also accept datasets with fewer individuals, such as for rare or endangered species, or hard-to-obtain samples.
  • For pool seq data: We recommend at least 40 individuals per pool and 80x coverage per pool, with at least 20 pools.
  • Please note that we are interested in all species, regardless of whether there is strong population structure or local adaptation.
  • If there are Indigenous interests in these data, we only wish to receive sample and data where there has been Prior and Informed Consent.
• A reference genome exists
• Sufficient metadata for each sample, including the latitude, longitude, depth, and time of sampling.
  • Ideally, historical environmental data is also available for each sample (one of the goals of this project will be to determine how to summarize this data in a standardized way). Currently we do not have specific requirements for the resolution or minimum time span of historical environmental data, but please be prepared to list sources of relevant environmental data when you submit your samples.
• Optional: trait data associated with each sample

Data submission workflow

Get started by filling out our form: Intent to Contribute a Dataset. Note that you do not have to have the samples or sequences in hand to fill out this form; by filling out this form you will be included in communications about the datasets and become eligible for sequencing awards.

We are in the process of publishing our data submission workflow on MarineOmics, a dynamic website for sharing protocols and best principles for marine genomics research.