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6 results for “molecular biomonitoring”
Data supplementing the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal
<p>These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal</p> <p>The directory contains the following files:</p> <p>1<strong>5 fastq files raw reads (5 mock communities, 3 replicates)</strong><strong>.rar </strong>- contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>15 fastq files information.xlsx</strong> :</p> <p>- contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq file.</p> <p>- contains the information of the proportion of the 8 diatoms species (%) used to create the 5 mock communities (estimated from microscopy).</p>
Data supplementing the article "Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal
<p>These data supplement the article "Enhancing DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal</p> <p>The directory contains the following files:</p> <p><strong>278 (139 x 2 replicates) samples fastq files.rar </strong>- contains the 278 fastq files provided by the sequencing platform with demultiplexed and contig DNA reads corresponding to the 139 samples with 2 sequencing replicates (A and B).</p> <p><strong>Counts_diatoms.xlsx </strong>- contains the morphological inventories with species list (Omnidia code) and valve abundances for the 139 samples.</p> <p><strong>Sites_list.xlsx </strong>- contains information regarding the 139 samples, including: River name, GPS coordinates, code used for molecular analysis and corresponding to sequencing fastq names.</p>
Data supplementing the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal
<p>These data supplement the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal.</p> <p>The directory contains the following files:</p> <p><strong>464_samples_fastq_files_(mothur).rar </strong>- contains the 464 fastq files proceed together during the Mothur bioinformatics treatments to produce the OTUs and ISUs tables. As the contig and the demultiplexing steps were performed by the sequencing platform, there is 1 fastq file per sample. From this 464 samples OTU/ISU tables, only information regarding 76 samples were used in this study and are listed in the "<strong>76_samples_list_(mothur).xlsx" </strong>file<strong>.</strong></p> <p><strong>76_samples_list_(mothur).xlsx </strong>- contains the information regarding the 76 samples used to create the OTUs and ISUs tables presented in the paper.</p> <p><strong>76_samples_R1_R2_fastq_files(DADA2).rar - </strong>contains the raw demultiplexed fastq files (R1.fastq and R2.fastq) for each of the 76 samples used in this study to produce the ESVs table using the DADA2 bioinformatics pipeline.</p>
A molecular method for biomonitoring of an exotic plant-pest: leafmining for environmental DNA
<p><span>1. Understanding how invasive species respond to novel environments is limited by a lack of sensitivity and throughput in conventional biomonitoring methods.<i> </i>Arthropods in particular are often difficult to monitor due to their small size, rapid lifecycles, and/or visual similarities with co-occurring species<i>. </i>This is true for the agromyzid leafminer fly, <i>Liriomyza sativae</i>, a global pest of vegetable and nursery industries that has recently established in Australia. </span></p> <p><span>2. A robust method based on environmental DNA (eDNA) was developed exploiting traces of DNA left inside 'empty' leaf mines, which are straightforward to collect and persist longer in the environment than the fly. This extends the window of possible diagnosis to at least 28 days after a leaf mine becomes empty. The test allowed for visually indistinguishable leafmining damage caused by <i>L. sativae</i> to be genetically differentiated from that of other flies. </span></p> <p><span> 3. Field application resulted in the identification of new local plant hosts for <i>L. sativae</i>, including widely distributed weeds and common garden crops, which has important implications for the pest's ability to spread. Moreover, the test confirmed the presence of a previously unknown population of <i>L. sativae</i> on an island in the Torres Strait. </span></p> <p>4. The developed eDNA method is likely to become an important tool for <i>L. sativae</i> and other leafmining species of biosecurity significance, which, historically, have been difficult to detect, diagnose and monitor. More generally, eDNA is emerging as a highly sensitive and labour-efficient surveillance tool for difficult to survey species to improve outcomes for agricultural industries, global health, and the environment.</p>
Data from: Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring
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A molecular method for biomonitoring of an exotic plant-pest: leafmining for environmental DNA
Open the record for dataset details and reuse information.
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