Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

The Roles of Bacteria and Fungi in Plant Nutrition

The Roles of Bacteria and Fungi in Plant Nutrition

Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.

Uncertainty in Measurement: Reading Instruments

Uncertainty in Measurement: Reading Instruments

Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Overview of Fungi

Overview of Fungi

Fungi are a diverse group of eukaryotes more closely related to animals than other eukaryotes. Fungal cell walls comprise chitin, a polysaccharide that provides structural strength, and glucans, which contribute to flexibility and integrity. Other polysaccharides, such as mannans and galactosans, may supplement or replace chitin in some fungi. These adaptations, along with their preference for acidic environments and tolerance for high osmotic pressure, enable fungi to thrive in various...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Nanopore Data-Driven Near-T2T Genome Assembly of <i>Hippophae rhamnoides</i> ssp. <i>mongolica</i> Rousi and Its Complex Annotation.

Plants (Basel, Switzerland)·2026

Same author

Transcriptomic data of seven flax varieties contrasting in lodging resistance.

Frontiers in plant science·2026

Same author

Progress in Flax Genome Assembly from Nanopore Sequencing Data.

Plants (Basel, Switzerland)·2026

Same author

Whole-genome sequencing of Russian poplars to understand relationships within the genus <i>Populus</i> L.

Frontiers in plant science·2026

Same author

Gene Expression and Fatty Acid Composition in Sea Buckthorn Seeds and Pulp During Fruit Development of Different Varieties.

International journal of molecular sciences·2025

Same author

Discovery of Hub Genes Involved in Seed Development and Lipid Biosynthesis in Sea Buckthorn (<i>Hippophae rhamnoides</i> L.) Using UID Transcriptome Sequencing.

Plants (Basel, Switzerland)·2025

Same journal

Correction: Thaochan et al. Fungal-Infected Weeds: A Potential Source of Leaf Spot Disease in Rubber Trees from Southern Thailand. <i>J. Fungi</i> 2025, <i>11</i>, 220.

Journal of fungi (Basel, Switzerland)·2026

Same journal

Distinct Phenotype and Secondary Metabolite Profile Mark a Dominant <i>Aspergillus flavus</i> Outbreak Strain.

Journal of fungi (Basel, Switzerland)·2026

Same journal

Morphology, Chemistry, and Phylogeny Reveal Two New Species of the Genus <i>Lecidella</i> (Ascomycota, Lecanoraceae) from Anhui Province, China.

Journal of fungi (Basel, Switzerland)·2026

Same journal

Unlocking the Biocontrol Potential of Indigenous Soil Fungi: High-Performing Strains of <i>Beauveria bassiana</i> and <i>Metarhizium robertsii</i> Against the Tomato Leafminer <i>Tuta absoluta</i>.

Journal of fungi (Basel, Switzerland)·2026

Same journal

Unraveling CARD9 Mutations in Deep Dermatophytosis: A Genetic Gateway to Fungal Invasion and Immune Dysfunction.

Journal of fungi (Basel, Switzerland)·2026

Same journal

Draft Genome and Comparative Analysis of a <i>Cutaneotrichosporon jirovecii</i>-Related Yeast Recovered from a Human Fecal Sample.

Journal of fungi (Basel, Switzerland)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 28, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

T2T Colletotrichum lini Genomes with Hifiasm: ONT R9 and R10 Read Processing and Assembly Guidelines for Fungi.

Elizaveta A Ivankina¹, Ekaterina M Dvorianinova¹, Alexander A Arkhipov^1,2

¹Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.

Journal of Fungi (Basel, Switzerland)

|January 27, 2026

Summary

This summary is machine-generated.

Optimized Oxford Nanopore Technologies (ONT) sequencing and Hifiasm assembly parameters enable complete telomere-to-telomere (T2T) genome assemblies for fungal pathogens like Colletotrichum lini. This facilitates genomic studies and understanding of flax anthracnose disease.

Keywords:

Colletotrichum lini Nanopore R9.4.1 and R10.4.1 flow cells T2T genome assembly anthracnose basecalling tools flax pathogen read processing

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

Published on: March 31, 2017

Related Experiment Videos

Last Updated: Jan 28, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

Published on: March 31, 2017

Area of Science:

Genomics
Bioinformatics
Mycology

Background:

Telomere-to-telomere (T2T) genome assembly is crucial for understanding complex fungal pathogen genomes.
Colletotrichum lini causes significant flax anthracnose disease, necessitating detailed genomic analysis.

Purpose of the Study:

To optimize guidelines for T2T genome assembly using Oxford Nanopore Technologies (ONT) sequencing data.
To evaluate different basecalling tools, read filtration strategies, and genome coverage levels for improved assembly quality.

Main Methods:

Analyzed ONT R9.4.1 and R10.4.1 sequencing data from four C. lini strains.
Compared Guppy and Dorado basecallers, quality/length read filtration (Q10/Q15, 5kb/10kb), and coverage (5x-160x).
Utilized Hifiasm 0.25.0 assembler with the --ont module for genome assembly.

Main Results:

Dorado basecalling improved read quality and telomere resolution, especially with R10.4.1 data.
Optimal assembly achieved with moderate coverage (40-65x) and specific filtration (Q15/5kb for R10.4.1, Q10/5kb for R9.4.1).
Achieved T2T/near-T2T assemblies (53.7-56.1 Mb), 12-13 chromosomes, complete mitochondrial genomes, and >98.5% BUSCO completeness.

Conclusions:

Optimized ONT data preprocessing and Hifiasm assembly yield high-quality T2T genomes for C. lini.
Established a robust framework for fungal genome assembly using ONT technology.
Findings support future research on genomic variation and pathogenicity in Colletotrichum species.