Related Experiment Video
Updated: Jun 16, 2026
06:53
Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants
Published on: May 5, 2023
Hidden Fungal DNA Structures May Shape Sequencing Outcomes.
1Faculty of Natural Sciences, University of Stirling, Stirling, UK.
Summary
Fungal DNA is often missed in sequencing due to cell walls and complex structures. Understanding these challenges can improve DNA detection and fungal biology research.
Area of Science:
- Mycology
- Genomics
- Bioinformatics
Background:
- Shotgun metagenomics frequently under-detects fungal DNA.
- Physical barriers like melanized cell walls and complex DNA structures may impede detection.
- Oxford Nanopore Technologies sequencing faces challenges with native fungal DNA, including pore clogging and translocation issues.
Purpose of the Study:
- To investigate the reasons behind the under-detection of fungal DNA in metagenomic sequencing.
- To explore the impact of fungal DNA structural complexities on sequencing technologies like Oxford Nanopore.
- To enhance the accuracy and scope of fungal DNA detection in various biological samples.
Main Methods:
- Analysis of under-detection patterns in shotgun metagenomic datasets.
- Investigation of Oxford Nanopore Technologies sequencing behavior with native fungal DNA.
- Characterization of physical and structural properties of fungal DNA relevant to sequencing.
Main Results:
- Fungal DNA under-detection is linked to cell wall composition and DNA conformation.
- Specific structural features of fungal DNA cause pore clogging and aberrant translocation dynamics during Nanopore sequencing.
- These challenges are likely due to intrinsic, currently undescribed, fungal DNA properties.
Conclusions:
- Addressing physical and structural barriers is crucial for improving fungal DNA detection.
- Further research into fungal DNA architecture can enhance sequencing accuracy.
- Understanding these sequencing complexities will advance fungal biology and genomics.
Related Concept Videos
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
01:05Maxam-Gilbert Sequencing
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
02:54Evolutionary Relationships through Genome Comparisons
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...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...