Abstract
Diatoms play a key role in water quality assessments and algae bloom. However, taxonomic confusion often exists for diatoms, and morphological characters are extremely diverse for species identification. DNA barcoding with multiple genetic markers can contribute much to diatom diversity investigation. In this study, we employed sequences of four genetic markers (COI, rbcL, SSU, and LSU) to discriminate diatom strains from both marine and freshwater environments of China, by tree, distance, and character-based barcoding methods. The available published diatom sequences were also incorporated into our new sequences. A total of 93 rbcL, 81 COI, 83 SSU, and 75 LSU sequences of diatom samples were obtained in this study. The multiple genetic markers discriminated most species clearly. The identification of species by micrographic observation was generally consistent with the DNA barcoding analysis except that some potential cryptic species were revealed by DNA barcoding. The COI, rbcL, and LSU sequences all showed high taxonomic resolution at the species level by phylogenetic and character-based analysis. Some potential identification errors in public diatom sequences were also found. The phylogenetic and character-based analysis revealed consistent species identification and showed clearer species discrimination than the distance-based method. In conclusion, our study evaluated the efficiency of four genetic markers in barcoding 11 genera within Bacillariophyta isolated from China and complemented many diatom reference sequences to public databases.
Highlights
Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments and are believed to be responsible for around one-fifth of primary productivity on earth and the occurrence of blooms (Bowler et al, 2008; Casteleyn et al, 2010)
A total of 93 rbcL, 81 COI, 83 SSU, and 75 LSU sequences of diatom samples were obtained in this study (Supplementary Table 1)
The identification of species for each strain by micrographic observations was consistent with the identification by DNA barcoding of all the four gene loci, except that some potential cryptic species were found within some species
Summary
Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments and are believed to be responsible for around one-fifth of primary productivity on earth and the occurrence of blooms (Bowler et al, 2008; Casteleyn et al, 2010). Diatoms are frequently used for water quality assessments for marine as well as freshwater environments (Kawecka and Olech, 1993; Spaulding and McKnight, 1999). There are, estimated 200,000 diatom species, living in terrestrial, freshwater, and marine systems as benthos or phytoplankton (Dam et al, 1994; Potapova and Charles, 2007; Zalack et al, 2010; Hamsher et al, 2011). Diatom-based indices require unambiguous identification at the species level. The species identification of diatoms is time-consuming and needs in-depth knowledge of organisms under investigation, such as bacteria (Zhang et al, 2018). Taxonomic confusion often exists for diatoms, while a large number of morphological characters are extremely diverse (Evans et al, 2007)
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