A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes

LA Amaral-Zettler, EA McCliment, HW Ducklow… - PloS one, 2009 - journals.plos.org
Background Massively parallel pyrosequencing of amplicons from the V6 hypervariable
regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess …

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

A Behnke, M Engel, R Christen, M Nebel… - Environmental …, 2011 - Wiley Online Library
Initial environmental pyrosequencing studies suggested highly complex protistan
communities with phylotype richness decisively higher than previously estimated. However …

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

A Zhan, M Hulák, F Sylvester, X Huang… - Methods in Ecology …, 2013 - Wiley Online Library
Concerns regarding the rapid loss of endemic biodiversity, and introduction and spread of
non‐indigenous species, have focused attention on the need and ability to detect species …

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

SM Huse, L Dethlefsen, JA Huber, DM Welch… - PLoS …, 2008 - journals.plos.org
Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal
RNA (SSU rRNA) genes can sample a microbial community two or three orders of …

Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity

N Taib, JF Mangot, I Domaizon, G Bronner… - PLoS One, 2013 - journals.plos.org
Recent advances in next-generation sequencing (NGS) technologies spur progress in
determining the microbial diversity in various ecosystems by highlighting, for example, the …

IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

I Lagkouvardos, D Joseph, M Kapfhammer, S Giritli… - Scientific reports, 2016 - nature.com
Abstract The SRA (Sequence Read Archive) serves as primary depository for massive
amounts of Next Generation Sequencing data and currently host over 100,000 16S rRNA …

Characterization of the 18S rRNA gene for designing universal eukaryote specific primers

K Hadziavdic, K Lekang, A Lanzen, I Jonassen… - PloS one, 2014 - journals.plos.org
High throughput sequencing technology has great promise for biodiversity studies.
However, an underlying assumption is that the primers used in these studies are universal …

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

V Kunin, A Engelbrektson, H Ochman… - Environmental …, 2010 - Wiley Online Library
Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has
revealed that the extent of rare microbial populations in several environments, the 'rare …

Evaluating and improving small subunit rRNA PCR primer coverage for bacteria, archaea, and eukaryotes using metagenomes from global ocean surveys

J McNichol, PM Berube, SJ Biller, JA Fuhrman - Msystems, 2021 - Am Soc Microbiol
Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and
comprehensively profile natural microbiomes, representing a critically important tool for …

Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes

AAY Lie, Z Liu, SK Hu, AC Jones, DY Kim… - Applied and …, 2014 - Am Soc Microbiol
Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger
sequencing for characterizing the diversity of natural microbial communities. Despite this …