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      Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

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          Abstract

          Recent advances in molecular sequencing technology and the increased availability of fieldable laboratory equipment have provided researchers with the opportunity to conduct real-time or near real-time gene-based biodiversity assessments of aquatic ecosystems. In this study, we developed a workflow and portable kit for fieldable environmental DNA sequencing (FeDS) and tested its efficacy by characterizing the breadth of jellyfish (Medusozoa) taxa in the coastal waters of the Upper and Lower Florida Keys. Environmental DNA was isolated from seawater collection events at eight sites and samples were subjected to medusozoan 16S rRNA gene and metazoan mitochondrial cytochrome oxidase 1 gene profiling via metabarcoding onsite. In total, FeDS yielded 175,326 processed sequence reads providing evidence for 53 medusozoan taxa. Our most salient findings revealed eDNA from: (1) two venomous box jellyfish (Cubozoa) species, including taxa whose stings cause the notorious Irukandji envenomation syndrome; (2) two species of potentially introduced stalked jellyfish (Staurozoa); and (3) a likely cryptic species of upside-down jellyfish (Scyphozoa). Taken together, the results of this study highlight the merits of FeDS in conducting biodiversity surveys of endemic and introduced species, and as a potential tool for assessing envenomation and/or conservation-related threats.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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

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                Author and article information

                Journal
                Frontiers in Marine Science
                Front. Mar. Sci.
                Frontiers Media SA
                2296-7745
                April 13 2021
                April 13 2021
                : 8
                Article
                10.3389/fmars.2021.640527
                35685121
                fe5bcb0f-05cf-453e-8a3d-47bb8b6835b0
                © 2021

                Free to read

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

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