Related Experiment Video
Updated: Mar 21, 2026
08:09
An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
Published on: September 15, 2015
9.3K
Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data
Manon Mireille Geerts1, Manuel Curto2,3,4, Andrew J Alverson5
1Eco-Evo-Devo and Conservation of Fishes, Department of Biology, KU Leuven, Leuven, Belgium.
Molecular Ecology Resources
|March 20, 2026
Summary
Leveraging genome assembly graphs with GetOrganelle uncovers hidden microeukaryotic diversity in environmental DNA (eDNA) data. Manual graph disentanglement successfully recovered complete organellar genomes, improving taxonomic resolution.
Area of Science:
- Environmental DNA (eDNA) Metagenomics
- Microbial Eukaryotic Genomics
- Bioinformatics and Assembly
Background:
- Genome assembly graphs offer insights into contig connectivity, crucial for enhancing genome assembly completeness.
- Microeukaryotic diversity remains underrepresented in public databases, hindering comprehensive ecological and evolutionary studies.
- Environmental DNA (eDNA) sequencing is a powerful tool for biodiversity assessment, but challenges remain in assembling genomes from complex mixtures.
Purpose of the Study:
- To demonstrate the utility of GetOrganelle for assembling organellar genomes from freshwater eDNA metagenomic datasets.
- To showcase the effectiveness of manual assembly graph disentanglement for recovering complete microeukaryotic genomes.
- To reveal previously hidden microeukaryotic diversity and improve taxonomic resolution using eDNA data.
Main Methods:
- Application of GetOrganelle for organellar genome assembly on three freshwater eDNA metagenomic datasets.
- Manual disentanglement of assembly graphs to resolve mixed-species complexity.
- Assembly quality assessment using sequence identity, gene order conservation, and phylogenetic analysis.
Main Results:
- GetOrganelle alone produced fragmented scaffolds from mixed-species eDNA samples.
- Manual disentanglement successfully recovered complete organellar genomes, including plastomes of Stephanodiscus hantzschii and a potentially novel Cyclotella species.
- Effective genome recovery was achieved even at low microeukaryote abundances.
- The integrated approach provided robust species-level resolution, surpassing traditional binning methods.
Conclusions:
- Mining eDNA metagenomic data with GetOrganelle and manual graph analysis is a powerful strategy for discovering hidden microeukaryotic diversity.
- This approach significantly enhances taxonomic resolution for microeukaryotes, addressing limitations in current reference databases.
- The methodology is particularly valuable for studying underrepresented microeukaryotic groups in environmental samples.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
7.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.2K
00:58Genomic DNA in Eukaryotes
53.9K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
53.9K
03:36Genome Annotation and Assembly
21.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.4K
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
17.4K
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...
17.4K
01:24Diversity of Archaea II
616
Archaea, one of the three domains of life, exhibit remarkable diversity and adaptability, thriving in both extreme and moderate environments. Historically, most identified archaea have been classified into two major phyla: Euryarchaeota and Crenarchaeota. However, recent molecular studies have expanded this classification to include three additional phyla: Thaumarchaeota, Nanoarchaeota, and Korarchaeota, each exhibiting unique characteristics and ecological roles.Thaumarchaeota: Mesophiles...
616
01:27Diversity of Archaea III
426
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...
426