Related Experiment Video
Updated: Dec 31, 2025
07:54
Manipulation of Ploidy in Caenorhabditis elegans
Published on: March 15, 2018
11.4K
Unzipping haplotypes in diploid and polyploid genomes
Xingtan Zhang1,2, Ruoxi Wu1, Yibin Wang1
1Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Computational and Structural Biotechnology Journal
|January 8, 2020
Summary
Haplotype phasing separates homologous chromosomes in diploid and polyploid genomes. This review covers methods and experimental advances for accurate genome phasing, crucial for understanding genetic variation.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Diploid genomes have two homologous chromosome copies, while polyploid genomes have more.
- Reference genome assemblies often collapse haplotypes, overlooking allelic variants.
- Haplotype phasing is vital for studying compound heterozygotes, heterosis, and evolution.
Purpose of the Study:
- To review current alignment-based and assembly-based haplotype phasing methods.
- To discuss recent experimental approaches for enhancing genome phasing.
- To highlight the growing importance of haplotype phasing in genomic research.
Main Methods:
- Review of alignment-based phasing techniques.
- Review of assembly-based phasing strategies.
- Analysis of experimental methods for haplotype resolution.
Main Results:
- Existing methods for diploid and polyploid genome phasing are categorized.
- Recent experimental advancements improve phasing accuracy.
- Haplotype phasing is increasingly essential for biological and clinical insights.
Conclusions:
- Full haplotype phasing is becoming a standard in genomic studies.
- Accurate phasing resolves complex genetic questions.
- The field is moving towards routine, comprehensive genome phasing.
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
17.8K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
17.8K
02:04Polytene Chromosomes
10.8K
Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also...
10.8K
02:37Gene Duplication and Divergence
7.7K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
7.7K
02:26Comparing Copy Number Variations and SNPs
18.5K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.5K
02:54Evolutionary Relationships through Genome Comparisons
6.8K
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...
6.8K
02:08Gene Conversion
10.5K
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...
10.5K