Estimating Protistan Diversity Using High-Throughput Sequencing

J Eukaryot Microbiol. 2015 Sep-Oct;62(5):688-93. doi: 10.1111/jeu.12217. Epub 2015 Apr 25.

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; V4 tag sequencing; biogeography; microbial eukaryotes; protists.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Eukaryota / genetics*
  • Genes, rRNA
  • Genetic Variation*
  • High-Throughput Nucleotide Sequencing*
  • Molecular Sequence Data
  • Phylogeny
  • RNA, Ribosomal, 18S / genetics
  • Sequence Analysis, DNA

Substances

  • RNA, Ribosomal, 18S

Associated data

  • GENBANK/KJ757035
  • GENBANK/KJ764638