Dataset: Ca. Aquarickettsia rohweri transcriptomes

Name: Sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome data from host Acropora cervicornis colonies collected at Looe Key, Lower Florida Keys from Apr to Jun of 2019
Published: 2024-05-24
Keywords: RNA-seq, coral reef, Rickettsiales, oceans

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Cite This Dataset

Spatial Extent: N:24.66164 E:-81.4543 S:24.66164 W:-81.4543

Florida Keys, USA

Temporal Extent: 2019-05

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)

Lauren Speare (Oregon State University, OSU)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-05-24

Restricted:

Validated:

Current State:

Data not available

Sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome data from host Acropora cervicornis colonies collected at Looe Key, Lower Florida Keys from Apr to Jun of 2019

Abstract:

This dataset contains sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome sequences housed at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA1048415. All host colonies (Acropora cervicornis genotype ML-50) were collected from the same location, the Mote Marine Laboratory in situ coral nursery in Looe Key, Lower Florida Keys between April and June of 2019. The Rickettsiales-like bacterial parasite, 'Candidatus' Aquarickettsia rohweri (NCBI:txid2602574) is a ubiquitous coral symbiont that is strongly linked to coral disease susceptibility in staghorn coral, and is undergoing positive selection across the Caribbean. Although ‘Ca.’ A. rohweri is a putative parasite, little is known about the activity of this bacterium in coral tissue. We performed a transcriptomic analyses of ‘Ca.’ A. rohweri populations during a 6-week nutrient exposure experiment. ‘Ca.’ A. rohweri energy scavenging genes and those potentially involved during habitat transition are significantly upregulated during enrichment. Specifically, transcripts involved in signaling, virulence, two-component systems, and nutrient import genes are elevated under higher nutrients. These data support the predicted role of ‘Ca.’ A. rohweri as a highly active nutrient-responsive A. cervicornis parasite and provide a glimpse at the mechanism of induced disease susceptibility while implicating nutrient exposure in its horizontal transmission.

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Description

These Ca. Aquarickettsia rohweri transcriptome data were published in Speare et al, (2023, doi: 10.1101/2023.06.08.544262) and are part of NCBI BioProject PRJNA1048415.

Closely related data also part of the same NCBI BioProject were published in Klinges et al. (2023, doi: 10.1093/femsec/fiac013) which published the experiment and accompanying data (16S, coral health status, coral growth rate) from the same samples.

Methods & Sampling

Fragments (~5cm) of Acropora cervicornis genotype ML-50 (Coral Sample Registry accession: fa13971c-ea34-459e-2f13-7bfddbafd327, LSID (urn:lsid:marinespecies.org:taxname:206989)) were collected from the Mote Marine Laboratory in situ coral nursery in Looe Key between April and June of 2019. Prior to experimental manipulation, fragments were allowed to acclimate to aquarium conditions for seven days. Nutrient enrichment was performed four times a day for 42 days (six weeks). Coral fragments were sacrificed for sampling: prior to nutrient exposure (T0), and after six weeks. Using sterile bone cutters, tissue was scraped from each fragment (avoiding the apical tip) and added directly to 2 mL tubes containing 0.5ml DNA/RNA shield (Zymo Research) and Lysing Matrix A (MP Biomedicals, 0.5 g garnet matrix and one 1/4" ceramic sphere). Tubes were immediately preserved at -80°C until further processing. Total RNA was extracted from 500 μl of tissue slurry using the E.Z.N.A.® DNA/RNA Isolation Kit (Omega Bio-Tek) and then stored at -80°C until further processing. Residual DNA contamination was removed from RNA isolates using the RQ1 RNase-Free DNase (Promega). Ribosomal RNA was removed using equal parts ‘plant leaf’, ‘human/mouse’ and ‘bacteria’ Ribo-Zero kits (Illumina). RNA quality and concentration were verified by BioAnalyzer (Agilent Technologies, Santa Clara, CA) and quantitative PCR, respectively. cDNA library prep and sequencing was performed at Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform. Three biological replicates for each treatment were sequenced (n=9).

Instruments:

Mote Marine Lab flow-through seawater raceways and 4.7L tanks: held corals during experiment
boiler and chiller: controlled aquarium temperature
Sterile bone cutters: used to collect coral tissue from each fragment
-80°C Freezer: used to keep samples at a low temp prior to processing
BioAnalyzer (Agilent Technologies, Santa Clara, CA): used to verify RNA quality and concentration
Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform: used for sample sequencing

Data Processing Description

Description of how the related sequence data at NCBI were processed and analyzed for the results publication Speare et al. (2023):

Quality scores were calculated for each sequence using FastQC and MultiQC; low-quality scores (average score <20 across 5bp) were removed. Adapters were trimmed using bbduck (BBTools User Guide); successful trimming was confirmed using FastQC/MultiQC. Forward and reverse reads were then interleaved using reformat (BBTools User Guide), mapped to the ‘Ca.’ A. rohweri genome using BowTie2, and counted using HTSeq-count. The limit of detection for each gene was one read per gene. The vegan package in R was used to perform principal coordinates analysis (PCoA) using the Bray-Curtis dissimilarity index, PerMANOVA using the Adonis function, and beta-diversity using the permutest.betadisper function. Differential expression analysis was performed through DeSeq2. Data were graphed in Graphpad Prism and edited for publication using Inkscape 1.0.

BCO-DMO Processing

* Sheet 1 of submitted file "NCBI_data_A_rohweri_transcriptomes_2024.xlsx" was imported into the BCO-DMO data system for this dataset. Metadata lines above the data table were incorporated as additional data columns.
* Additional columns added from NCBI Biosample information for organism and host.
* Additional collection information columns added from metadata provided in email correspondence (lat,lon, collection year and month range description).

* 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]

More Information about this dataset

Funding Sources

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

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 3000 platform

Supplied Description:

Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform: used for sample sequencing

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.

Bioanalyzer

Supplied Name: BioAnalyzer (Agilent Technologies, Santa Clara, CA)

Supplied Description:

Used to verify RNA quality and concentration

Instrument Type

Generic Name: Bioanalyzer

Generic Description:

A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_name	description	unitless	sample
BioSample_Accession	BioSample accession number in the National Center for Biotechnology Information (NCBI) BioSample database	unitless	BioSample
SRA	Sample accession number in the NCBI Sequence Read Archive (SRA)	unitless	SRA_sample
BioProject	BioProject identifier at NCBI	unitless	BioProject
Data_Type	Date type description (e.g. Raw sequence reads)	unitless	sample_descrip
Scope	Sample scope description	unitless	sample_descrip
Organism	Organism description for the sequence accessions	unitless	sample_descrip
Collected_Host_Organism	Host organism collected	unitless	sample_descrip
Strain	strain (as shown with NCBI BioSample)	unitless	sample_descrip
isolation_source	Isolation source (from the host organism)	unitless	sample_descrip
Treatment	Description of treatment conditions sampled organism was exposed to	unitless	treatment
Collection_lat	Collection site latitude (of host)	decimal degress	lat
Collection_lon	Collection site longitude (of host)	decimal degrees	lon
Collection_Year	Collection year (of host) Format: %Y	unitless	year
Collection_date_note	Description of month and year range during which sampling took place	unitless	sample_descrip

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Database

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Dataset: Ca. Aquarickettsia rohweri transcriptomes