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Data Brief
2019 Oct 20;26:104405. doi: 10.1016/j.dib.2019.104405.
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High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of naturally occurring and laboratory aquaculture green sea urchins Lytechinus variegatus.
Hakim JA
,
Morrow CD
,
Watts SA
,
Bej AK
.
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We present high-throughput amplicon sequence (HTS) datasets of the microbial metacommunity DNA of the gut tissue and the gut digesta of naturally occurring (n = 3) and laboratory aquaculture (n = 2) green sea urchins, Lytechinus variegatus. The HTS datasets were generated on an Illumina MiSeq by targeting the amplicons of the V4 region of the 16S rRNA gene. After the raw sequences were quality checked and filtered, 88% of the sequence reads were subjected to bioinformatics analyses to generate operation taxonomic units (OTUs), which were then verified for saturation by using rarefaction analysis at a 3% sequence variation. Further, the OTUs were randomly subsampled to the minimum sequence count values. Then, the FASTA-formatted representative sequences of the microbiota were assigned taxonomic identities through multiple databases using the SILVA ACT: Alignment, Classification and Tree Service (www.arb-silva.de/aligner). The HTS datasets of this metagenome can be accessed from the BioSample Submission Portal (https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject IDs PRJNA291441 and PRJNA326427.
Fig. 1. Rarefaction curve analysis of the HTS data showing the number of OTUs (Y-axis) plotted against total number of sequences (X-axis) per sample. OTUs were determined by using the PhyloToAST (v1.4) taxonomy condensing workflow, which is integrated into QIIME (v1.9.1). Samples were rarefied to the minimum sequence count across all samples for downstream bioinformatics analysis. Data were plotted using Microsoft Excel Software (Seattle, WA, USA).
Fig. 2. Relative abundance distribution of taxa at the highest resolution determined for the merged biological replicates using multiple taxonomic databases. The FASTA-formatted representative sequences determined by the PhyloToAST (v1.4) workflow integrated into QIIME (v1.9.1) were aligned to multiple databases using the SILVA ACT: Alignment, Classification and Tree Service (www.arb-silva.de/aligner). Taxonomic assignments were performed using the SSU (Small Subunit) category and the Least Common Ancestor (LCA) method with the following databases: SILVA, Ribosomal Database Project (RDP), The All-Species Living Tree (LTP) project, Greengenes (GG), and the European Molecular Biology Laboratory (EMBL). Sequences aligned with a similarity threshold below 70% were discarded. The top 25 taxa from each database were merged based on their common taxonomic assignments at the specific level of classification.
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