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      Comparison of the biodiversity of epiphytic diatoms in the Euphrates-Tigris rivers using morphological and metabarcoding analyses

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          Abstract

          The Euphrates-Tigris catchment area is one of the major drainage basins in the Middle East but climate change, overuse of waters and subsequent salinization has brought this region to the brink of ecological devastation. The aim of this study was to investigate the biodiversity of epiphytic diatoms in Iraq, for the first time using a combination of morphological and metabarcoding methods. 47 samples were collected at six sampling sites along the Rivers Tigris and Euphrates in northern Basra, Southern Iraq, during the summer of 2019 (dry season) and winter of 2020 (rainy season). The composition of the epiphytic diatoms in each sample was compared with both methods. The microscopic-morphological analysis of the environmental samples resulted in the identification of 284 infrageneric taxa in 59 genera. For the metabarcoding analysis the V4 region of the 18S marker gene was used and resulted in 1454 ASVs (Amplicon sequence variants) comprising 54 genera and 108 species with several ASVs belonging to the same taxa. The non-metric multidimensional scaling (NMDS) plots for morphology showed a clear seasonal effect in the diatom community composition, while the NMDS plots for 18SV4 analyses did not show a seasonal effect in community composition for the same samples. The incomplete taxonomic reference database for the studied sites turned out to be the major limitation of the molecular approach. Nevertheless, the combination of morphological and molecular methods increased the detection and identification of the diatom assemblages and laid the foundation for understanding their biodiversity in this region.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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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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                Journal
                Metabarcoding and Metagenomics
                MBMG
                Pensoft Publishers
                2534-9708
                December 13 2024
                December 13 2024
                : 8
                Article
                10.3897/mbmg.8.135082
                f4c5278f-2bda-48be-8686-e7cf61479c5e
                © 2024

                http://creativecommons.org/licenses/by/4.0/

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