Related Experiment Video
Updated: Sep 29, 2025
13:03
Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
10.8K
De novo phasing resolves haplotype sequences in complex plant genomes
Ji-Yoon Guk1, Min-Jeong Jang1, Jin-Wook Choi1
1Department of Environmental Horticulture, University of Seoul, Seoul, Korea.
Plant Biotechnology Journal
|March 25, 2022
Summary
Genome phasing separates complex DNA into distinct haplotypes, revealing crucial genetic differences. This review covers tools and findings for plant genomes, highlighting phasing
Area of Science:
- Genomics
- Bioinformatics
Background:
- Most de novo genome assemblies represent consensus sequences, masking important haplotype variations.
- Genome phasing is a crucial assembly method for resolving heterozygous eukaryotic genomic regions into haplotype-specific assemblies.
- This approach is vital for understanding biological characteristics influenced by allelic differences.
Purpose of the Study:
- To review the principles and characteristics of widely used genome phasing tools.
- To examine the impact of haplotype-resolved assemblies on downstream analyses in plants.
- To identify limitations and suggest future directions for de novo genome phasing.
Main Methods:
- Review of operating principles for TrioCanu, FALCON-Phase, and ALLHiC.
- Analysis of downstream applications of haplotype-resolved plant genome assemblies.
- Identification of current limitations and future research needs in genome phasing.
Main Results:
- Significant haplotype differences were observed in plant genomes, including chromosomal rearrangements and sequence insertions.
- Allelic expression variations between haplotypes contribute to species-specific biological traits.
- Freely available tools like TrioCanu, FALCON-Phase, and ALLHiC are instrumental for genome phasing.
Conclusions:
- Haplotype-resolved assemblies reveal genetic variations critical for understanding plant biology.
- Addressing current limitations in genome phasing methods is essential for broader adoption.
- This review facilitates researchers' use of genome phasing for complex plant genomes.
Related Concept Videos
02:53Conservative Site-specific Recombination and Phase Variation
6.2K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
6.2K
02:54Evolutionary Relationships through Genome Comparisons
6.3K
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...
6.3K
02:37Restarting Stalled Replication Forks
5.9K
DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
5.9K
01:59The Phragmoplast
5.4K
Cell division is essential for organismal growth and development. In animal cells, the central spindle and its associated proteins form the midbody, a structure that has an essential role in cytokinesis. In plants, the central spindle, along with the microtubules, actin, and other cell components, matures into the phragmoplast, which is necessary for cytokinesis. Unlike the stationary midbody, the phragmoplast expands centrifugally, eventually leading to the formation of the new cell wall.
The...
The...
5.4K
02:08Gene Conversion
10.0K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.0K
02:31Homologous Recombination
5.0K
5.0K