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Alveolates are a group of organisms recognized by the presence of alveoli, which are cytoplasmic sacs located beneath the cell membrane. While their function remains uncertain, alveoli may help regulate water balance by controlling how much water enters and leaves the cell. In dinoflagellates, these structures may serve as armor plates. There are three major types of alveolates: ciliates, which move using cilia; dinoflagellates, which use flagella for movement; and apicomplexans, which are...
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Rhizaria are a diverse group of unicellular protists characterized by their threadlike cytoplasmic extensions known as pseudopodia. These structures aid in both locomotion and feeding, giving Rhizaria an amoeboid appearance. Their amoeboid morphology once led to taxonomic confusion, but molecular phylogenetics has clarified their evolutionary placement and emphasized their shared use of pseudopodia despite divergent lineages.This clade comprises diverse lineages such as Chlorarachniophyta,...
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Excavata is a diverse group of protists that includes both chemoorganotrophic and phototrophic species, with some thriving in anaerobic environments. Among the key groups within Excavata are diplomonads and parabasalids, which are flagellated protists that lack mitochondria and chloroplasts. These microorganisms typically inhabit anoxic environments, such as the intestines of animals, where they exist either symbiotically or as parasites, relying on fermentation for energy production. Some...
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Crenarchaeota, a prominent phylum of Archaea, is remarkable for its ability to thrive in extreme environments characterized by high temperatures and acidity. These microorganisms inhabit sulfuric hot springs, volcanic systems, and submarine hydrothermal vents, where temperatures often exceed 100°C. The unique adaptations of Crenarchaeota not only allow survival under such extreme conditions but also provide insights into the mechanisms of life in primordial Earth-like...
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Hyperthermophilic archaea are a group of extremophiles thriving at temperatures above 80°C, often in hydrothermal vents and volcanic soils where conditions surpass the boiling point of water. At such temperatures, proteins, membranes, and DNA in most organisms degrade, but hyperthermophiles have evolved remarkable adaptations to maintain stability and function.Unique Cellular FeaturesHyperthermophilic membranes are composed of a monolayer of biphytanyl tetraether lipids, which resist...
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Estimating Protistan Diversity Using High-Throughput Sequencing.

Sarah K Hu1, Zhenfeng Liu1, Alle A Y Lie1

  • 1Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA.

The Journal of Eukaryotic Microbiology
|April 9, 2015
PubMed
Summary
This summary is machine-generated.

Sequencing the V4 hypervariable region of the 18S rRNA gene using reads over 400 nucleotides provides taxonomic resolution comparable to full-length sequences for protistan biodiversity studies.

Keywords:
18S rRNA geneV4 tag sequencingbiogeographymicrobial eukaryotesprotists

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Area of Science:

  • Microbial Ecology
  • Molecular Biology
  • Bioinformatics

Background:

  • Protistan biodiversity is often assessed using 18S rRNA gene sequencing.
  • Concerns exist regarding the taxonomic resolution of short sequencing reads compared to full-length sequences.

Purpose of the Study:

  • To evaluate the impact of sequence length and target regions on protistan diversity estimations.
  • To determine if shorter reads can achieve similar ecological interpretations as full-length 18S rRNA gene sequences.

Main Methods:

  • In silico analysis of 7,432 full-length 18S rRNA gene sequences.
  • Comparison of taxonomic resolution across various sequence lengths and hypervariable regions (e.g., V4).

Main Results:

  • Sequences longer than 400 nucleotides, including the V4 region, yielded results comparable to full-length sequences.
  • High-throughput sequencing is approaching the resolution of whole gene sequences for protistan diversity.

Conclusions:

  • Targeted sequencing of specific 18S rRNA gene regions (like V4) with sufficient length can reliably characterize protistan biodiversity.
  • Short-read sequencing technologies are becoming viable alternatives for comprehensive protistan diversity assessments.