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Diversity of Protists II01:27

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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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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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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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Amoebozoa represent a diverse group of terrestrial and aquatic protists that utilize lobe-shaped pseudopodia for locomotion and feeding. This characteristic differentiates them from the Rhizaria, which possess threadlike pseudopodia. The primary classifications within Amoebozoa include gymnamoebas, entamoebas, and the plasmodial and cellular slime molds. Phylogenetic evidence indicates that Amoebozoa diverged from a lineage that ultimately gave rise to fungi and animals.Gymnamoebas and...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Unveiling Protist Composition and Diversity Patterns With eDNA Metabarcoding: Comparing Short- and Long-Read

Dimitra-Ioli Skouroliakou1,2, Deborah W E Dupont3,4, Yelle Vandenboer3

  • 1IFREMER, DYNECO Plouzané France.

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Long-read sequencing offers deeper taxonomic insights for environmental DNA (eDNA) metabarcoding, improving protist community analysis. This method enhances biodiversity monitoring by providing greater detail than short-read sequencing.

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Area of Science:

  • Marine biology
  • Genomics
  • Ecology

Background:

  • Environmental DNA (eDNA) metabarcoding is crucial for biodiversity monitoring.
  • Short-read (SR) sequencing has limitations in taxonomic assignment depth for complex organisms like protists.
  • Long-read (LR) sequencing technologies present an underutilized alternative for studying protist communities.

Purpose of the Study:

  • To compare the effectiveness of SR versus LR metabarcoding for analyzing protist communities.
  • To evaluate taxonomic assignment depth and community composition patterns between SR and LR approaches.
  • To assess the utility of LR sequencing for enhancing ecological insights in marine monitoring.

Main Methods:

  • Comparative metabarcoding study of protist communities using SR (Illumina) and LR (Oxford Nanopore Technologies) sequencing.
  • Targeted amplicons of the 18S rRNA gene (V4 region for SR, V4-V5 for LR).
  • Analysis of diversity patterns, taxonomic assignment, and community composition along a coastal-offshore gradient.

Main Results:

  • General congruence in community composition at higher taxonomic levels between SR and LR methods.
  • LR metabarcoding provided greater taxonomic annotation depth at lower taxonomic ranks.
  • LR data revealed less overrepresentation of dinoflagellates and unique detections of key protist genera.

Conclusions:

  • LR metabarcoding complements SR approaches by offering enhanced taxonomic resolution and ecological insights.
  • LR sequencing shows significant potential for improving routine plankton monitoring and biodiversity assessments.
  • Advancements in sequencing technologies, particularly LR, are vital for future ecological studies.