title: Estimating Protistan Diversity Using High-Throughput Sequencing.
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.
authors: Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA.
authors: Sarah K
authors: SK
authors: Hu
authors: Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA.
authors: Zhenfeng
authors: Z
authors: Liu
authors: Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA.
authors: Alle A Y
authors: AA
authors: Lie
authors: Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA.
authors: Peter D
authors: PD
authors: Countway
authors: Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA.
authors: Diane Y
authors: DY
authors: Kim
authors: Mount St. Mary's College, Los Angeles, California, 90049, USA.
authors: Adriane C
authors: AC
authors: Jones
authors: Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA.
authors: Rebecca J
authors: RJ
authors: Gast
authors: Environmental Research Institute, School of Science, University of Waikato, Hamilton, 3240, New Zealand.|College of Earth and Ocean Science, University of Delaware, Newark, Delaware, 19716, USA.
authors: S Craig
authors: SC
authors: Cary
authors: College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA.
authors: Evelyn B
authors: EB
authors: Sherr
authors: College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA.
authors: Barry F
authors: BF
authors: Sherr
authors: Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA.
authors: David A
authors: DA
authors: Caron
mesh_terms: D056890:Eukaryota / Q000235:genetics*; D020459:Genes, rRNA; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012337:RNA, Ribosomal, 18S
keywords: 18S rRNA gene; V4 tag sequencing; biogeography; microbial eukaryotes; protists