The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
Visualitza/Obre
Autor/a
Rimet, Frédéric
Abarca, Nelida
Bouchez, Agnès
Kusber, Wolf-Henning
Jahn, Regine
Kahlert, Maria
Keck, François
Kelly, Martyn G.
Mann, David G.
Piuz, André
Tapolczai, Kalman
Vasselon, Valentin
Zimmermann, Jonas
Data de publicació
2018-02-27ISSN
1802-5439
Resum
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.
Tipus de document
Article
Versió del document
Versió publicada
Llengua
English
Matèries (CDU)
504 - Ciències del medi ambient
Pàgines
18
Publicat per
Czech Phycological Society
Publicat a
Fottea
Citació
Rimet, Frederic, Nelida Abarca, Agnes Bouchez, Wolf-Henning Kusber, Regine Jahn, Maria Kahlert, and Francois Keck et al. 2018. "The Potential Of High-Throughput Sequencing (HTS) Of Natural Samples As A Source Of Primary Taxonomic Information For Reference Libraries Of Diatom Barcodes". Fottea 18 (1): 37-54. Palacky University Olomouc. doi:10.5507/fot.2017.013.
Número de l'acord de la subvenció
EC/COST/CA15219/EU/Developing new genetic tools for bioassessment of aquatic ecosystems in Europe/DNAqua-Net
Programa
Aigües Marines i Continentals
Aquest element apareix en la col·lecció o col·leccions següent(s)
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