RT Journal Article
SR Electronic
A1 Rimet, Frédéric
A1 Abarca, Nelida
A1 Bouchez, Agnès
A1 Kusber, Wolf-Henning
A1 Jahn, Regine
A1 Kahlert, Maria
A1 Keck, François
A1 Kelly, Martyn G.
A1 Mann, David. G.
A1 Piuz, André
A1 Trobajo, Rosa
A1 Tapolczai, Kalman
A1 Vasselon, Valentin
A1 Zimmermann, Jonas
T1 The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
JF Fottea
YR 2018
VO 18
IS 1
SP 37
OP 54
DO 10.5507/fot.2017.013
UL https://fottea.czechphycology.cz/artkey/fot-201801-0004.php
AB 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.