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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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RNA-seq03:21

RNA-seq

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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...
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Next-generation Sequencing03:00

Next-generation Sequencing

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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....
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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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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...
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Related Experiment Video

Updated: Jan 13, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Sequencing of mRNA from Whole Blood using Nanopore Sequencing

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Progress in Flax Genome Assembly from Nanopore Sequencing Data.

Elena N Pushkova1, Alexander A Arkhipov1,2, Nadezhda L Bolsheva1

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

Plants (Basel, Switzerland)
|January 10, 2026
PubMed
Summary
This summary is machine-generated.

Researchers generated high-quality flax (Linum usitatissimum L.) genome assemblies using Oxford Nanopore Technologies (ONT) sequencing. These new assemblies improve upon existing references, aiding genetic research and crop improvement for this multipurpose plant.

Keywords:
HifiasmLinum usitatissimumNanoporeflaxgenome assemblylong-read sequencingtelomere-to-telomere

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Area of Science:

  • Genomics
  • Plant Science
  • Bioinformatics

Background:

  • Genome assembly quality has significantly improved with third-generation sequencing and advanced bioinformatics.
  • Flax (Linum usitatissimum L.) is a valuable multipurpose crop, but high-quality genome references are crucial for its genetic advancement.

Purpose of the Study:

  • To generate high-quality, near-telomere-to-telomere (T2T) genome assemblies for two flax varieties, K-3018 and Svyatogor.
  • To assess the quality of these assemblies against existing flax genome references.

Main Methods:

  • Utilized Oxford Nanopore Technologies (ONT) simplex R10.4.1 sequencing data.
  • Employed the Hifiasm algorithm optimized for ONT reads.
  • Validated assemblies using Hi-C contact maps and Illumina sequencing data.

Main Results:

  • Successfully assembled the K-3018 genome (491.1 Mb) and Svyatogor genome (497.8 Mb), each comprising mostly complete chromosomes with telomeric repeats.
  • The K-3018 and Svyatogor assemblies exceed the quality of the current reference flax genome (variety T397).
  • Comparative analysis indicated general similarity between flax genomes at the chromosome level with minor large-scale variations.

Conclusions:

  • Achieved two near-T2T flax genome assemblies using ONT simplex R10.4.1 reads and Hifiasm, without PacBio HiFi or optical maps.
  • High-quality flax genomes are vital for advancing genetic research, assessing diversity, and developing breeding and genome editing strategies.