Assigning taxonomy and traits to DNA sequences of river diatoms in a region with limited taxonomic knowledge using the updated and annotated reference library Diat.barcode

Abstract

We present a new version of a barcoding reference library dedicated to diatoms, Diat.barcode v12, with newly published sequences, annotated with ecological, and biological traits (size class, life forms, ecological guilds, etc) and curated by a college of experts. Diat.barcode incorporates rbcL data on all diatoms, though freshwater taxa are better represented. We used this library in two different areas, one where the taxonomic coverage of the library was good (mainland France) and another where it was poor (French Guyana) with about 320 diatom samples collected for river monitoring across both regions. We show that a direct bioinformatic assignment of environmental sequences to traits (ecological guilds, habitats, morphology) has great potential in French Guyana where species knowledge is poor and therefore the proportion of assigned environmental sequences is much lower (12.8%) than trait assignation (30%). We used co-correspondence analyses to show that, unlike mainland France where all species and trait assignation datasets were significantly correlated, in French Guyana only 7 out of 13 trait categories showed a significant correlation. This indicates a significant loss of ecological information through species assignment in French Guyana. Consequently, directly assigning environmental sequences to traits can be useful and provide more ecological information in regions with poor taxonomic knowledge because of the many rbcL sequences without taxonomic assignations.