Estimating Protistan Diversity Using High-Throughput Sequencing. Academic Article

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

• Hu, Sarah

published proceedings

• J Eukaryot Microbiol

altmetric score

• 0.75

author list (cited authors)

• Hu, S. K., Liu, Z., Lie, A., Countway, P. D., Kim, D. Y., Jones, A. C., ... Caron, D. A.

citation count

• 52

complete list of authors

• Hu, Sarah K||Liu, Zhenfeng||Lie, Alle AY||Countway, Peter D||Kim, Diane Y||Jones, Adriane C||Gast, Rebecca J||Cary, S Craig||Sherr, Evelyn B||Sherr, Barry F||Caron, David A

publication date

• September 2015

publisher

• Wiley  Publisher

published in

• Journal of Eukaryotic Microbiology  Journal

keywords

• 18s Rrna Gene
• Biogeography
• Eukaryota
• Genes, Rrna
• Genetic Variation
• High-Throughput Nucleotide Sequencing
• Microbial Eukaryotes
• Molecular Sequence Data
• Phylogeny
• Protists
• RNA, Ribosomal, 18S
• Sequence Analysis, DNA
• V4 Tag Sequencing

PubMed Central ID

• 25851049

Digital Object Identifier (DOI)

• 10.1111/jeu.12217

start page

• 688

end page

• 693

volume

• 62

issue

• 5

URL

• http://dx.doi.org/10.1111/jeu.12217