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Estimating Protistan Diversity Using High‐Throughput Sequencing |
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| Authors: | Sarah K Hu Zhenfeng Liu Alle A Y Lie Peter D Countway Diane Y Kim Adriane C Jones Rebecca J Gast S Craig Cary Evelyn B Sherr Barry F Sherr David A Caron |
| Institution: | 1. Department of Biological Sciences, University of Southern California, Los Angeles, California, USA;2. Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA;3. Mount St. Mary's College, Los Angeles, California, USA;4. Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA;5. Environmental Research Institute, School of Science, University of Waikato, Hamilton, New Zealand;6. College of Earth and Ocean Science, University of Delaware, Newark, Delaware, USA;7. College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA |
| Abstract: | Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution as full‐length sequences. A total of 7,432 full‐length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations. Sequences that were longer than 400 nucleotides and included the V4 hypervariable region generated results similar to those derived from full‐length 18S rRNA gene sequences. Present high‐throughput sequencing capabilities are approaching protistan diversity estimation comparable to whole gene sequences. |
| Keywords: | 18S rRNA gene biogeography microbial eukaryotes protists V4 tag sequencing |