DNA metabarcoding data analysis

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Data Analysis ◽  
Dna Extraction ◽  
Illumina Sequencing ◽  
Molecular Methods ◽  
Sequencing Data ◽  
Ecological Processes ◽  
Operational Taxonomic Units ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
Illumina Sequencing Data

DNA metabarcoding generates huge amounts of data containing noise introduced by molecular methods. Chapter 8 “DNA metabarcoding data analysis” discusses the analytic steps and available software to curate and evaluate DNA metabarcoding data prior to final ecological analyses. It provides command lines to perform primary analyses of Illumina sequencing data with the OBITools, ranging from read assignment to samples to the formation of molecular operational taxonomic units (MOTUs) and their assignment to a taxon through comparison against reference databases. Chapter 8 also develops several methods to further curate sequencing data from contaminants or dysfunctional PCRs by using DNA extraction, PCR, and sequencing blank controls as well as PCR/biological replicates. It also presents several classical analyses to ensure that the diversity of the sample or the study site is appropriately covered. Finally, this chapter considers what conclusions on biodiversity and ecological processes can be really drawn from metabarcoding data.

scholarly journals PIMBA: a PIpeline for MetaBarcoding Analysis

2021 ◽  
Author(s):  
Renato R. M. Oliveira ◽  
Raissa L S Silva ◽  
Gisele L. Nunes ◽  
Guilherme Oliveira
Keyword(s):  
Environmental Samples ◽  
Next Generation Sequencing Data ◽  
Ecological Studies ◽  
Sequencing Data ◽  
Monitoring Method ◽  
Computational Tools ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
User Friendly ◽  
Generation Sequencing

DNA metabarcoding is an emerging monitoring method capable of assessing biodiversity from environmental samples (eDNA). Advances in computational tools have been required due to the increase of Next-Generation Sequencing data. Tools for DNA metabarcoding analysis, such as MOTHUR, QIIME, Obitools, and mBRAVE have been widely used in ecological studies. However, some difficulties are encountered when there is a need to use custom databases. Here we present PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases used by the softwares mentioned here. PIMBA is an open-source and user-friendly pipeline that consolidates all analyses in just three command lines.

scholarly journals Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Teresita M. Porter ◽  
Dave M. Morris ◽  
Nathan Basiliko ◽  
Mehrdad Hajibabaei ◽  
Daniel Doucet ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Beta Diversity ◽  
Ecological Integrity ◽  
Sequence Variants ◽  
Key Indicator ◽  
Pooled Dna ◽  
Dna Metabarcoding ◽  
Arthropod Fauna ◽  
Reference Databases ◽  
Arthropod Biodiversity

AbstractTerrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for arthropod biodiversity assessments from soil. Processing 15 individually collected soil samples recovered significantly higher median richness (488–614 sequence variants) than pooling the same number of samples (165–191 sequence variants) prior to DNA extraction, and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Beta diversity was robust to changes in methodological regimes. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.

scholarly journals Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92T Using Nanopore and Illumina Sequencing Data

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Michael M. Karl ◽  
Anja Poehlein ◽  
Frank R. Bengelsdorf ◽  
Rolf Daniel ◽  
Peter Dürre
Keyword(s):  
Carbon Monoxide ◽  
Genome Sequence ◽  
Illumina Sequencing ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequencing Data ◽  
Circular Chromosome ◽  
Content Type ◽  
Illumina Sequencing Data

ABSTRACT Here, we report the closed genome sequence of Clostridium formicaceticum, an Rnf- and cytochrome-containing autotrophic acetogen that is able to convert carbon monoxide to acetate using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (4.59 Mb).

scholarly journals QuicK-mer: A rapid paralog sensitive CNV detection pipeline

2015 ◽  
Author(s):  
Feichen Shen ◽  
Jeffrey Kidd
Keyword(s):  
High Throughput ◽  
Illumina Sequencing ◽  
Copy Number ◽  
Sequencing Data ◽  
Genome Copy ◽  
Genome Copy Number ◽  
Downstream Analysis ◽  
Cnv Detection ◽  
Illumina Sequencing Data ◽  
Control Regions

QuicK-mer is a unified pipeline for estimating genome copy-number from high-throughput Illumina sequencing data. QuicK-mer utilizes the Jellyfish application to efficiently tabulate counts of predefined sets of k-mers. The program performs GC-normalization using defined control regions and reports paralog-specific estimates of copy-number suitable for downstream analysis. The package is freely available at https://github.com/KiddLab/QuicK-mer

scholarly journals Identification of microRNAs in the green and red sectors of Amaranthus tricolor L. leaves based on Illumina sequencing data

2018 ◽  
Author(s):  
Shengcai Liu ◽  
Liyun Peng ◽  
Junfei Pan ◽  
Xiao Wang ◽  
Chunli Zhao ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Sequencing Data ◽  
Amaranthus Tricolor ◽  
Sequencing Platform ◽  
Transcriptome Database ◽  
Polymerase Chain ◽  
Illumina Sequencing Platform ◽  
Illumina Sequencing Data

Betalains are abundant in amaranth plants. Additionally, the betalain molecular structure and metabolic pathway differ from those of betanin in beet plants. To date, only a few studies have examined the regulatory roles of miRNAs in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 198 known and 41 novel miRNAs. Moreover, 216 miRNAs were distributed in 44 miRNA families, including miR156, miR159, miR160, miR166, miR172, miR319, miR167, miR396, and miR398. An analysis of all unigene sequences in an amaranth transcriptome database resulted in the detection of 493 target genes for the 239 screened miRNAs. The targets included SPL2, ARF18, ARF6, and NAC. A quantitative real-time polymerase chain reaction validation of 20 miRNAs and nine target genes revealed expression-level differences between the red and green sectors of amaranth leaves. This study involved the application of an Illumina sequencing platform to identify miRNAs regulating betalain metabolism in amaranth plants. The data presented herein may provide insights into the molecular mechanisms underlying the regulation of betalain biosynthesis in amaranth and other plant species.

scholarly journals New insights into Danube’s macroinvertebrate communities from DNA metabarcoding as part of the Joint Danube Survey 4 (JDS4)

2021 ◽  
Vol 4 ◽  
Author(s):  
Arne Beermann ◽  
Dominik Buchner ◽  
Florian Leese ◽  
Till-Hendrik Macher ◽  
Miroslav Ocadlik ◽  
...  
Keyword(s):  
Bulk Sample ◽  
Taxonomic Composition ◽  
Danube River ◽  
Taxonomic Resolution ◽  
Macroinvertebrate Communities ◽  
Operational Taxonomic Units ◽  
Sampling Campaign ◽  
Dna Metabarcoding ◽  
Assessment And Monitoring ◽  
Reference Databases

The Joint Danube Survey (JDS) is a multinational effort in monitoring Danube’s water quality, including its major tributaries. The Danube river stretches over a distance of 2,800 km and flows through or borders 10 different countries to which it is of utter importance as a source of potable water and hydrodynamic power. The JDS is conducted every 6 years and provides a unique opportunity to collect comprehensive data on both abiotic parameters and organisms and to raise awareness of the importance of water as a natural resource. As part of JDS and as a biological quality element in many monitoring programs worldwide, macroinvertebrates are monitored as indicators for various environmental conditions. However, due to their diverse taxonomic composition, associated difficulties with their morphology-based identification as well as their sheer abundance, macroinvertebrates are often analysed with a low taxonomic resolution (i.e., above species level). As an alternative, DNA metabarcoding offers a promising approach to capture this species diversity more accurately. Here, we used DNA metabarcoding to investigate the macrozoobenthic diversity of 46 sites from the latest JDS sampling campaign in 2019. To analyse macroinvertebrate diversity, bulk samples were taken by kick-net sampling and analysed using two different approaches, analysing the bulk sample fixative and analysing homogenised organisms from complete bulk samples. DNA metabarcoding of the sample fixative revealed 1,146 Operational Taxonomic Units (OTUs) and 231 species compared to 833 OTUs and 333 species from homogenised sample analysis. While more dipterans, in particular Chironomidae, were detected in fixative (136 species) than homogenised bulk (90 species) analyses, the latter picked up more Trichoptera (19 vs. 2), Amphipoda (10 vs. 4) and Bivalvia species (13 vs. 5). Even though these results of a DNA-based assessment deliver new insights into species richness and composition of Danube’s macroinvertebrate communities from the Danube source to its delta already, it is evident that the majority of OTUs was not assigned to species. While filling this lack of reference sequences poses a major challenge, the JDS consortium also offers a unique opportunity to complement reference databases in a multinational effort towards a more comprehensive Danube assessment and monitoring.

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