Related Experiment Video
Updated: Apr 21, 2026
12:08
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
7.3K
Dramatic improvement in genome assembly achieved using doubled-haploid genomes.
Hong Zhang1, Engkong Tan1, Yutaka Suzuki2
1Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
Scientific Reports
|October 28, 2014
Summary
Using doubled-haploid individuals significantly improves de novo genome assembly quality. This method enhances contig and scaffold sizes for more accurate genome analysis, particularly for large genomes.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- De novo assembly of large genomes remains challenging.
- High-quality genome sequences are crucial for biological research.
Purpose of the Study:
- To improve the quality of draft genome sequences.
- To evaluate the utility of doubled-haploid individuals in genome assembly.
Main Methods:
- Sequencing of wildtype and doubled-haploid Takifugu rubripes genomes using Illumina platform.
- Genome assembly using SOAPdenovo2 software.
- Comparative analysis of contig and scaffold metrics.
Main Results:
- A 5.4-fold improvement in N50 contig size was observed in doubled-haploid individuals.
- A 2.6-fold improvement in scaffold size was observed in doubled-haploid individuals.
- Demonstrated enhanced genome assembly quality with doubled-haploid approach.
Conclusions:
- Doubled-haploid individuals significantly enhance de novo genome assembly.
- This approach aids in achieving more accurate and complete genome analysis.
- The method is particularly beneficial for assembling large and complex genomes.
Related Concept Videos
03:36Genome Annotation and Assembly
16.5K
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.
16.5K
01:49Meiosis I
176.2K
Meiosis is a carefully orchestrated set of cell divisions, the goal of which—in humans—is to produce haploid sperm or eggs, each containing half the number of chromosomes present in somatic cells elsewhere in the body. Meiosis I is the first such division, and involves several key steps, among them: condensation of replicated chromosomes in diploid cells; the pairing of homologous chromosomes and their exchange of information; and finally, the separation of homologous chromosomes by...
176.2K
02:08Gene Conversion
9.2K
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...
9.2K
01:57Meiosis II
168.8K
Meiosis II is the second and final stage of meiosis. It relies on the haploid cells produced during meiosis I, each of which contain only 23 chromosomes—one from each homologous initial pair. Importantly, each chromosome in these cells is composed of two joined copies, and when these cells enter meiosis II, the goal is to separate such sister chromatids using the same microtubule-based network employed in other division processes. The result of meiosis II is two haploid cells, each...
168.8K
02:37Gene Duplication and Divergence
6.8K
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...
6.8K
01:29Nondisjunction
67.4K
During meiosis, chromosomes occasionally separate improperly. This occurs due to failure of homologous chromosome separation during meiosis I or failed sister chromatid separation during meiosis II. In some species, notably plants, nondisjunction can result in an organism with an entire additional set of chromosomes, which is called polyploidy. In humans, nondisjunction can occur during male or female gametogenesis and the resulting gametes possess one too many or one too few chromosomes.
67.4K