R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lénaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

doi:10.1093/database/baw016

Cited by 79 publications

(66 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The obtained DNA sequences are compared with those of known specimens recorded in a database (Taberlet et al 2012b). If the database is incomplete, algorithms are used to find the best taxonomic assignment for the query sequences within a certain threshold of sequence dissimilarity (Boyer et al 2016;Rimet et al 2016). Metabarcoding, combined with new high-throughput, next-generation sequencing (NGS) techniques such as Illumina amplicon sequencing, potentially provides a sufficiently high number of sequences compared to cloning and Sanger sequencing, to reveal the community composition adequately (Shokralla et al 2012;Taberlet et al 2012a).…”

Section: Introductionmentioning

confidence: 99%

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

et al. 2016

View full text Add to dashboard Cite

The Arctic treeline ecotone is characterised by a steep vegetation gradient from arctic tundra to northern taiga forests, which is thought to influence the water chemistry of thermokarst lakes in this region. Environmentally sensitive diatoms respond to such ecological changes in terms of variation in diatom diversity and richness, which so far has only been documented by microscopic surveys. We applied next-generation sequencing to analyse the diatom composition of lake sediment DNA extracted from 32 lakes across the treeline in the Khatanga region, Siberia, using a short fragment of the rbcL chloroplast gene as a genetic barcode. We compared diatom richness and diversity obtained from the genetic approach with diatom counts from traditional microscopic analysis. Both datasets were employed to investigate diversity and relationships with environmental variables, using ordination methods. After effective filtering of the raw data, the two methods gave similar results for diatom richness and composition at the genus level (DNA 12 taxa; morphology 19 taxa), even though there was a much higher absolute number of sequences obtained per genetic sample (median 50,278), compared with microscopic counts (median 426). Dissolved organic carbon explained the highest percentage of variance in both datasets (14.2 % DNA; 18.7 % morphology), reflecting the compositional turnover of diatom assemblages along the tundra-taiga transition. Differences between the two approaches are mostly a consequence of the filtering process of genetic data and limitations of genetic references in the database, which restricted the determination of genetically identified sequence types to the genus level. The morphological approach, however, allowed identifications mostly to species level, which permits better ecological interpretation of the diatom data. Nevertheless, because of a rapidly increasing reference database, the genetic approach with sediment DNA will, in the future, enable reliable Electronic supplementary material The online version of this article (doi:10.1007/s10933-016-9926-y) contains supplementary material, which is available to authorized users. 123J Paleolimnol DOI 10.1007/s10933-016-9926-y investigations of diatom composition from lake sediments that will have potential applications in both paleoecology and environmental monitoring.

show abstract

Section: Introductionmentioning

confidence: 99%

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

et al. 2016

View full text Add to dashboard Cite

show abstract

“…For detailed information on the studied strains see Table in the Supporting Information, and Rimet et al. (), Kelly et al. (), Mougin et al.…”

Section: Methodsmentioning

confidence: 99%

“…The TCC database also includes information about curated strains from NCBI (National Center for Biotechnology Information) (Rimet et al. ), and such strain information was also added to the present study when relevant. Altogether, rbc L barcodes were available for 66 strains in the TCC collection.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)

Kahlert

Kelly

Mann

et al. 2019

Journal of Phycology

Self Cite

View full text Add to dashboard Cite

This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA‐barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well‐defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.

show abstract

“…TCC culture collection hosts algal cultures, but also uncultured samples containing species of interest (as permanent slides, and raw and treated material). All metadata are stored in the open-access R-Syst::diatom reference database; a detailed description of this database and its management is given in Rimet et al (2016). Taxonomy, sequences, photos, sampler names, phenotypic data, etc., can be consulted and downloaded at: http:// www.rsyst.inra.fr/ Table 1 and Fig.…”

Section: Preparation Of the Library Of Amplicons And Hts Sequencingmentioning

confidence: 99%

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Rimet¹,

Abarca²,

Bouchez³

et al. 2018

Fottea

Self Cite

View full text Add to dashboard Cite

Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.

show abstract

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Cited by 79 publications

References 74 publications

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Contact Info

Product

Resources

About