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      Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791

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          Abstract

          Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.

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          Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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            phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

            Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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              Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

              16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of ‘best available’ primer pairs for Bacteria and Archaea for three amplicon size classes (100–400, 400–1000, ≥1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.
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                Author and article information

                Contributors
                Journal
                Data Brief
                Data Brief
                Data in Brief
                Elsevier
                2352-3409
                22 April 2023
                June 2023
                22 April 2023
                : 48
                : 109171
                Affiliations
                [a ]Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
                [b ]Department of Food Science and Nutrition, University of the Aegean, Lemnos 81400, Greece
                Author notes
                [* ]Corresponding author. argiriou@ 123456certh.gr
                Article
                S2352-3409(23)00290-1 109171
                10.1016/j.dib.2023.109171
                10189087
                37206897
                c8717013-73e4-40e1-85fe-2cb3f6d95e6a
                © 2023 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 31 December 2022
                : 29 March 2023
                : 17 April 2023
                Categories
                Data Article

                sea cucumber,echinoderms,holothuria tubulosa,whole genome sequencing,gastrointestinal tract microbiome,metagenomics,16s rrna,illumina

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