Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • BCO-DMO Processing Description
  • Problem Description
• Data Files
• Supplemental Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

Related NCBI BioProjects containing genomic/transcriptomic data from this study (see Supplemental Files for accession metadata):

mRNA sequencing from 48 A. cervicornis colonies differentially exposed to white band disease at multiple time points: NCBI BioProject PRJNA949884 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA949884)

Whole genome sequencing of DNA from 96 A. cervicornis colonies: NCBI BioProject PRJNA950067 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA950067)

Short and long read data and Genome Assembly for the Coral Restoration Foundation K2 genotype of A. cervicornis: NCBI BioProject PRJNA948411 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA948411)

Putative genotypes were collected on SCUBA from either the Coral Restoration Foundation nursery habitat (Florida) or from five natural reefs (Panama). Florida sampling took place in June 2021 and Panama sampling occurred in November 2021. At each location, ten replicate fragments from each putative genotype were spread across one of ten 18-liter recirculating tanks held at ambient seawater temperatures at each location’s flow-thru seawater system. Each fragment was experimentally lesioned with a waterpik to facilitate transmission (Gignoux-Wolfsohn et al. 2012). Five tanks were exposed to 50ml of disease slurry produced from 10 WBD infected coral fragments and five tanks were exposed to 50ml of healthy slurry from 10 healthy fragments. Slurries were produced by waterpiking disease or healthy coral tissue off the sampled corals in filtered seawater (FSW) and normalizing the slurry doses to a standard ocular density of 0.6 at 600nm. Exposed coral tanks were censused for disease twice daily at 6am and 6pm (local time, EST) for up to 7 days and disease coral fragments were pulled from tanks at the first signs of disease to prevent amplifying pathogen spread within each tank.

High molecular weight genomic DNA was extracted from all samples using the Zymo Quick-DNA 96 kit. Whole genome sequencing was produced for all putative genotypes using Illumina DNA Prep kit on two 150bp paired-end NovaSeq S4 runs. For the K2 genotype three libraries were prepared using Oxford Nanopore Technologies (ONT) kit SQK-LSK112. Two libraries were not size selected while the third included 20+kb PippenPrep size-selection. All ONT prepared libraries were sequenced separately on three Minion flow cells (FLO-MIN112). High-quality base-calling was performed using Guppy v6.1.7 (Oxford Nanopore Technologies). An additional four Illumina PCR-Free shotgun libraries were constructed using the DISCOVAR protocol to produce libraries with fragments between 400 and 600 bp (Love et al. 2016). KAPA PCR-free library kits were leveraged with the addition of a second round of 0.7x Agencourt AmPure XP SPRI bead cleanup post adapter ligation. Libraries were multiplexed and sequenced on a single rapid-run HiSeq 2500 flowcell with 250 bp paired-end sequencing. Finally, mRNA sequence data was obtained for 48 samples (including the K2 genotype) using NEBs unidirectional mRNA library preparations sequenced on an Illumina NEXTSEQ 550 platform.

Organism identifier (LSID):
Acropora cervicornis (urn:lsid:marinespecies.org:taxname:206989)

* Submitted file "exposure_experiment.csv" was imported into the BCO-DMO data system for this dataset.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores.  Can not start with a number]

NSF Award Abstract:

Coral disease outbreaks have radically altered the structure and function of tropical coral reefs worldwide. As progress has been made towards understanding the basic cause of many coral diseases, significant gaps remain in our knowledge of how corals respond to and resist disease infection, even as calls are being made for science to assist in coral evolution by selecting thermal or disease tolerant coral species or genotypes - often called "super corals". This project uses the endangered Caribbean staghorn coral Acropora cervicornis and White Band Disease (WBD) as a host-pathogen system to study the genetics of coral disease resistance. WBD epidemics decimated this key shallow-water Caribbean coral and led to its endangered listing. While the recovery of staghorn corals has been slow, data indicate that up to 15% or more of staghorn corals are highly disease resistant. This project uses modern genomic tools to identify genetic markers for staghorn coral disease resistance. The identification of genetic markers for disease resistance (i) provides needed information on the efficacy of "assisted evolution" for coral resiliency (ii) helps predict how well staghorn coral can resist future disease outbreaks, (iii) assists conservation efforts aimed at identifying and selecting corals with high disease resistance, and (iv) spurs the development of molecular assays for coral disease resistance. This research provides graduate and undergraduate training in the STEM fields of microbiology, genetics, and computational biology. The project is as a platform to develop outreach curricula to teach students about coral diseases and reef health, which are disseminated via Northeastern University's K-12 outreach program and the Smithsonian Tropical Research Institute's outreach program in Panama. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems.

It is increasingly becoming clear that the future of coral reefs depends on the resilience of reef-building corals to adapt or acclimate to their changing environment, which in turn requires that key traits like thermal tolerance and disease resistance are genetically heritable, identifiable, and quantifiable. Using staghorn corals and WBD as a model host-pathogen system, this project identifies the genetic underpinnings of disease resistance in Caribbean staghorn corals using state-of-the-art, multi-omic approaches linking patterns of variation across the staghorn coral genome, transcriptome and proteome. For Aim 1, genome-wide SNP variation from 200 staghorn coral genotypes from two populations [100 Florida; 100 Panama] is used to identify genomic regions associated with disease resistance using genome-wide association (GWA) analyses. For Aim 2, tank-based transmission experiments are used to profile key differences in the transcriptomic (mRNA and miRNA) and proteomic response of resistant versus susceptible staghorn corals during disease exposure. Mulit-omic data are analyzed using: (1) eQTL to link SNPs to mRNA expression, (2) miRNA-mRNA interactions and correlation networks to test for post-transcriptional gene regulation, and (3) network-based approaches. For Aim 3, 16s rDNA amplicon sequencing are used to identify changes in the staghorn coral microbiome due to disease resistance and exposure using microbial DNA from the resistant and susceptible corals used in the tank-based experiment (Aim 2). In addition to identify genetic markers associated with coral disease resistance, this study produces (1) the most complete multi-omic analysis of coral immunity and disease resistance to date, and (2) the first functional analyses of miRNA post-translational gene regulation in a cnidarian host-pathogen system. Data on the genetics of coral disease resistance provide valuable information on the efficacy of "assisted evolution" for coral resiliency. By using nursery raised staghorn corals from Florida, this project directly identifies highly disease resistant corals that can be used in the large-scale out planting efforts.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.