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10 results for “Orbicella faveolata”
Orbicella faveolata and O. franksi coral metagenome assemblies from the Lower Florida Keys region of Florida, USA
<div> <p>The enclosed files include mostly <em>Orbicella faveolata</em> and three <em>Orbicella franksi</em> coral metagenome assemblies collected from the Lower Keys in Florida’s Coral Reef, USA. Metadata for the files is included in this repository. Apparently healthy coral tissue cores were collected between May 28 and June 21, 2021. The DNA was extracted from the host and associated microorganisms and sequenced in a paired-end 150 bp format on an Illumina NovaSeq. Trimming and quality filtering of DNA sequence reads proceeded, followed by host and photoendosymbiotic dinoflagellate DNA removal. The host-cleaned reads were assembled individually by coral sample into longer contigs using MegaHit v1.1.4. The “Assembly_Fastas” zipped file contains 41 metagenome assemblies from the individual <em>Orbicella faveolata</em> corals and 3 assemblies from the individual <em>Orbicella franksi </em>colonies for a total of 44 assemblies. In addition, these assemblies were annotated with eggnog-mapper v2.1.6 to generate both predicted gene regions and annotation output files. The “Predicted_Gene_Fastas” zipped file contains nucleotide fasta files of the predicted gene regions for all 44 coral metagenome assemblies. The fasta header of each gene includes the contig ID it originated from in the associated “Assembly_Fasta”. The “Predicted_Gene_Annotations” zipped file contains either .csv or .xlsx files with the eggnog-mapper-based annotations. These files contain a “query contig” that corresponds to the contig ID in the fasta header of the “Predicted_Gene_Fasta”. </p> <p>In addition to individual assemblies, a co-assembly was generated that included all 41 <em>Orbicella faveolata</em> coral samples. Prior to co-assembly, further removal of eukaryotic DNA proceeded by splitting the indiviudual assemblies into eukaryotic and prokaryotic content with the program EukRep v0.6.7, followed by mapping of the host-clean reads to the eukaryotic DNA to remove them. The eukaryote-clean reads from all 41 corals were input into MegaHit to generate a co-assembly. The co-assembly is included (FLK_OFAV_MG_coassembly_final.contigs.fa). Predicted genes from the co-assembly were generated with Prodigal v2.6.3 and the nucleotide fasta of the output is included in this repository (FLK_OFAV_MG_pred.fna). Like with the indiviudal assemblies, eggnog-mapper was used to generate annotations of the predicted genes from Prodigal (FLK_OFAV_MG.emapper.annotations.xlsx). Additionally, the abundance of each predicted gene was generated using Salmon to map the eukaryote-clean reads to the predicted genes. The number of reads (counts) for each gene across each coral sample were aggregated as integers into one table and included in this repository (FLK_OFAV_MG_pred_NumReads.tsv). </p> </div> <div> <p>These data were processed and generated by Julie Meyer’s Lab at the University of Florida, using funding from the Florida Department of Environmental Protection. </p> </div>
PacBio HiFi de-novo assembled genome and mitochondrial genome for Orbicella faveolata
<p>Final assembly using Funannotate of <i>Orbicella faveolata</i> from PacBio HiFi reads. For full methods please see the publication. </p>
Orbicella faveolata coral metagenome assemblies from the ECA region of Florida, USA
<p>The enclosed files include <em>Orbicella faveolata</em> coral metagenome assemblies collected from the Coral Ecosystem Conservation Area (ECA) in southeast Florida, USA. Metadata for the files including region of collection and associated NCBI accession numbers is included in this repository as the metadata file. Apparently healthy coral tissue cores were collected between May 28 and June 21, 2021. The DNA was extracted from the host tissue and mucus and sequenced in a paired-end 150 bp format on an Illumina NovaSeq. Trimming and quality filtering of DNA sequences proceeded, followed by host and endosymbiotic dinoflagellate DNA removal. The host-cleaned reads were assembled individually by coral sample into longer contigs using MegaHit v1.1.4. The “Assembly_Fastas” zipped file contains 45 metagenome assemblies from the individual <em>Orbicella faveolata</em> corals. In addition, these metagenome assemblies were annotated with eggnog-mapper v2.1.6 to generate both predicted gene regions and annotation output files. The “Predicted_Gene_Fastas” zipped file contains nucleotide fasta files of the predicted gene regions for the 45 coral metagenome assemblies. The fasta header of each gene includes the contig ID it originated from in the associated “Assembly_Fastas”. The “Predicted_Gene_Annotations” zipped file contains either .csv or .xlsx files with the eggnog-mapper-based annotations. These files contain a “query contig” that corresponds to the contig ID in the fasta header of the “Predicted_Gene_Fastas”. </p> <p>These data were processed and generated by Julie Meyer’s Lab at the University of Florida, using funding from the Florida Department of Environmental Protection.</p>
Data for Coral Growth and Sequences for Cyclin-E and G3P Primers for Orbicella faveolata
<p>Cyclin-E and glyceraldehyde 3-phosphate dehydrogenase primer sets were constructed using Primer3 from an annotated<br> transcriptome (Polato et al., 2011). For each sample and gene, reactions were performed in triplicate on a Step One Plus qPCR<br> machine (Applied Biosystems, Waltham, MA), using cDNA of <em>Orbicella faveolata</em> (Ellis & Solander, 1786) as a template. Singlepeak melt curve analysis was performed to test for nonspecific amplification products, but limited sample prevented primer<br> efficiency analysis. To verify primer specificity, the two primers were tested on cDNA from <em>Casseopia xamachana</em>, with no<br> amplification being observed.</p>
Screening of bacterial diversity by 16S rRNA metabarcoding in Orbicella faveolata healthy and with Black Band Disease
<p>Screening of bacterial diversity by 16S rRNA metabarcoding in Orbicella faveolata healthy and with Black Band Disease</p>
Data and code for "Sediment source and concentration influence larval performance of the threatened coral Orbicella faveolata" submitted to PlosOne
<p>This repository contains data and analysis scripts for the manuscript:</p> <p><strong>Sediment source and concentration influence larval performance of the threatened coral Orbicella faveolata</strong></p> <p><strong>Authors</strong>: XM Serrano, S Rosales, MW Miller, A Palacio-Castro, O Williamson, A Gomez and AC Baker</p> <p><strong>Journal: </strong>PlosOne</p> <p>The aim of this study was to investigate the performance of coral larvae from an important Caribbean reef-building coral species listed under the Endangered Species Act (<em>Orbicella faveolata</em>) exposed to sediments collected near a recently dredged Port in southeast Florida (Port Miami) vs. reef sediments collected where their parents originated from (Florida Keys). We tested whether sediments can affect the survival, settlement and respiration of coral larvae, and hypothesized detrimental effects in all of these parameters for sediments collected near the Port, regardless of dosing (low vs. high sediment treatments).</p>
Data from: Population structure and connectivity of the mountainous star coral, Orbicella faveolata, throughout the wider Caribbean region
Open the record for dataset details and reuse information.
Understanding differential heat tolerance of the threatened mountainous star coral Orbicella faveolata from inshore and offshore reef sites in the Florida Keys using gene network analysis
GEO Series GSE225085. Orbicella faveolata. 48 samples. Type: Expression profiling by high throughput sequencing.
Understanding differential heat tolerance of the threatened coral Orbicella faveolata from transplanted reef sites in the Florida Keys using gene network analysis
GEO Series GSE233773. Orbicella faveolata. 56 samples. Type: Expression profiling by high throughput sequencing.
Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis
GEO Series GSE92695. Orbicella faveolata. 6 samples. Type: Expression profiling by array.
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