Dataset: Acropora cervicornis transcriptomes: nutrient- and disease-exposed

Name: Acropora cervicornis transcriptomes: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022
Published: 2024-04-09
Keywords: transcriptome, disease, nutrient, immune, oceans

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Cite This Dataset

Spatial Extent: N:24.56257 E:-81.40009 S:24.56257 W:-81.40009

Mote Marine Laboratory Elizabeth Moore International Center for Coral Reef Research & Restoration. Research conducted in ex situ aquaria

Temporal Extent: 2022-06-29 - 2022-07-27

Project:

Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility (Coral Rickettsiales)

Principal Investigator:

Rebecca Vega Thurber (Oregon State University, OSU)

Co-Principal Investigator:

Erinn M. Muller (Mote Marine Laboratory, Mote)

Scientist:

Grace J. Klinges (Mote Marine Laboratory, Mote)

BCO-DMO Data Manager:

Lynne M. Merchant (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-04-09

Restricted:

Yes

Release Date:

2024-12-02

Validated:

Current State:

Preliminary and in progress

Acropora cervicornis transcriptomes: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022

Abstract:

We confirmed data from previous studies showing that genotypes of Acropora cervicornis dominated by the coral parasite Aquarickettsia are more susceptible to White Band Disease than genotypes with diverse microbiomes. However, in a study with ramets from genotypes exhibiting each microbiome profile, we found that the strongest predictor of disease development was prior exposure to increased thermal stress that occurred independent of the study on Florida’s reef during the experiment. While no ramets of the coral genotype with a diverse microbiome developed disease after exposure to nutrient enrichment, seven ramets of this genotype developed disease after exposure to elevated temperatures and subsequent disease challenge. Two ramets exposed to elevated temperatures and not exposed to disease also died, suggesting that temperature alone could have been fatal to this genotype. An equal number of ramets exposed to elevated nutrients and elevated temperatures developed disease in the genotype dominated by Aquarickettsia. To evaluate the effect of Aquarickettsia infection; nutrient enrichment; disease exposure; and the combination of these factors on coral immune function, we conducted RNAseq on 42 samples to an averaging sequencing depth of 22,168,890.6 reads per sample (paired-end).

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Methods & Sampling

Samples of coral tissue, skeleton, and mucus were taken from two genotypes of Acropora cervicornis prior to nutrient enrichment (n = 20 per genotype), prior to disease exposure (n = 18 per genotype), and at various stages during disease development. All surviving ramets at one week after disease exposure were sampled. To sample each coral, 6-8 polyps were excised using a flame-sterilized blade and placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for RNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. RNA from each sample was isolated utilizing the E.Z.N.A. DNA/RNA Isolation Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. RNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were shipped on dry ice to the Oklahoma Medical Research Foundation NGS Core, where RNA cleanup, precipitation, and polyA selection was performed. Libraries were prepared using the IDT xGen RNA Library kit. Final QC was performed using KAPA qPCR and Agilent Tapestation to confirm rRNA content, and libraries were sequenced on a NovaSeq 6000 using S4 chemistry.

Data Processing Description

A total of 42 samples were successfully sequenced on an Illumina NovaSeq 6000 with S4 chemistry and PE 150 bp reads. Prior to quality filtering, an average single-end read depth of 11,084,445.3 +/- 970,330.08 was produced from sequencing. After filtration, an average of 10,954,237.2 +/- 982,482.11 reads remained per read direction. From quality filtered sequences, 72.54% of single end reads mapped to the A. cervicornis transcriptome using STAR. Quantification using Salmon resulted in 24,875 genes having at least one count across all samples, with subsequent filtering (less than 1 count in >10 samples) reducing this to 12,913 genes for downstream analysis. Of reads not aligning to the A. cervicornis transcriptome, an average of 22.54% aligned to the Symbiodinium (Clade A) reference transcriptome using STAR. Quantification using Salmon yielded counts for 73,112 transcripts, with 26,225 of these retained for downstream analysis after filtering (less than 1 count in greater than 10 samples). Analysis of differentially expressed transcripts is ongoing.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1923926
NSF Division of Ocean Sciences	OCE-1923836

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina Nova Seq 6000

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Thermo Scientific NanoDrop spectrophotometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermo Scientific NanoDrop spectrophotometer

Acronym: NanoDrop spectrophotometer

Generic Description:

A Thermo Scientific NanoDrop spectrophotometer provides microvolume quantification and purity assessments of DNA, RNA, and protein samples. The results appear in seconds. NanoDrop spectrophotometers work on the principle of ultraviolet-visible spectrum (UV-Vis) absorbance. A series of Thermo Scientific NanoDrop spectrophotometers are manufactured by Thermo Fisher Scientific™ (https://www.thermofisher.com/us/en/home.html).

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Database

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Dataset: Acropora cervicornis transcriptomes: nutrient- and disease-exposed