Dataset Information

Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

ABSTRACT: DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.

SUBMITTER: Zimmermann J

PROVIDER: S-EPMC4180937 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

Zimmermann Jonas J Abarca Nelida N Enke Neela N Skibbe Oliver O Kusber Wolf-Henning WH Jahn Regine R

PloS one 20140929 9

DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 un ...[more]

PMID: 25265556

Similar Datasets

Project description:Partnering with people most affected by mental health problems can transform mental health outcomes. Citizen science as a research approach enables partnering with the public at a substantial scale, but there is scarce guidance on its use in mental health research. To develop best practise guidelines for conducting and reporting research, we conducted a systematic review of studies reporting mental health citizen science research. Documents were identified from electronic databases (n = 10), grey literature, conference proceedings, hand searching of specific journals and citation tracking. Document content was organised in NVIVO using the ten European Citizen Science Association (ECSA) citizen science principles. Best practise guidelines were developed by (a) identifying approaches specific to mental health research or where citizen science and mental health practises differ, (b) identifying relevant published reporting guidelines and methodologies already used in mental health research, and (c) identifying specific elements to include in reporting studies. A total of 14,063 documents were screened. Nine studies were included, from Australia, Belgium, Canada, Denmark, Netherlands, Spain, the UK, and the United States. Citizen scientists with lived experience of mental health problems were involved in data collection, analysis, project design, leadership, and dissemination of results. Most studies reported against some ECSA principles but reporting against these principles was often unclear and unstated. Best practise guidelines were developed, which identified mental health-specific issues relevant to citizen science, and reporting recommendations. These included citizen science as a mechanism for empowering people affected by mental health problems, attending to safeguarding issues such as health-related advice being shared between contributors, the use of existing health research reporting guidelines, evaluating the benefits for contributors and impact on researchers, explicit reporting of participation at each research stage, naming the citizen science platform and data repository, and clear reporting of consent processes, data ownership, and data sharing arrangements. We conclude that citizen science is feasible in mental health and can be complementary to other participatory approaches. It can contribute to active involvement, engagement, and knowledge production with the public. The proposed guidelines will support the quality of citizen science reporting.

Dataset Information

Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

Publications

Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets