Related Experiment Video
Updated: May 15, 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
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly
1Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai 200240, China.
BMC Systems Biology
|January 4, 2013
Summary
Optimizing hybrid assemblies of bacterial genomes, like Enterococcus faecium, requires careful selection of next-generation sequencing (NGS) data. Combining different NGS technologies, especially SOLiD, improves genome assembly continuity and cost-efficiency.
Area of Science:
- Genomics
- Bioinformatics
- Microbial Pathogenesis
Background:
- Bacterial genome sequencing is crucial for understanding pathogen virulence and strain relationships.
- Enterococcus faecium is a significant nosocomial pathogen often exhibiting antibiotic resistance.
- High genetic diversity in E. faecium poses challenges for next-generation sequencing (NGS) technologies.
Purpose of the Study:
- To investigate the properties and biases of different NGS technologies.
- To evaluate parameters influencing hybrid assembly outcomes using combined NGS data.
- To optimize hybrid assembly strategies for challenging bacterial genomes like E. faecium.
Main Methods:
- Sequencing of an E. faecium hospital strain using 454 GS-FLX, Illumina GAIIx, and ABI SOLiD4.0 platforms.
- Development of a pipeline to merge contigs from various NGS data for hybrid assemblies.
- Testing combinations and varying amounts of NGS data to optimize assembly continuity.
Main Results:
- Individual NGS assemblies reached a continuity ceiling, not improved by increased coverage alone.
- Each NGS technology exhibited intrinsic properties like base-calling errors and systematic biases.
- SOLiD data, when combined with other NGS data in a hybrid approach, significantly improved E. faecium genome assembly.
Conclusions:
- Characterized sequence data and assembly from individual NGS technologies.
- Identified optimized parameters for cost-efficient and continuous hybrid genome assembly.
- Provided guidelines for genomic studies of microorganisms using state-of-the-art sequencing.
More Related Videos
Related Concept Videos
03:36Genome 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.
01:08Evolution of Microbial Genome
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
03:00Next-generation Sequencing
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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
00:58Genomic DNA in Eukaryotes
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
00:46Genomic DNA in Prokaryotes
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic Diversity in Bacteria
Although bacterial genomes are much...