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Related Concept Videos

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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DNA Bacteriophages01:26

DNA Bacteriophages

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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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Cytoskeletal Proteins in Bacteria01:29

Cytoskeletal Proteins in Bacteria

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Bacterial cells were initially considered simple, randomly organized structures lacking a cytoskeleton. However, the discovery of cytoskeleton homologs in bacteria led to the change of this opinion. Bacterial cytoskeletal filaments regulate the cell shape, cell polarity, cell division, and partitioning of plasmids during cell division. It was later discovered that bacterial cytoskeletal proteins, mainly actin and tubulin homologs, are diverse compared to their eukaryotic counterparts. On the...
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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

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The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
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Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
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Related Experiment Video

Updated: Sep 23, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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B-assembler: a circular bacterial genome assembler.

Fengyuan Huang1,2, Li Xiao3, Min Gao1,3

  • 1Informatics Institute, Heersink School of Medicine, the University of Alabama at Birmingham, AL, 35294, Birmingham, USA.

BMC Genomics
|May 13, 2022
PubMed
Summary
This summary is machine-generated.

B-assembler accurately assembles circular bacterial genomes using long or hybrid sequencing reads. This new tool overcomes challenges in bacterial genome assembly, improving downstream analysis.

Keywords:
Bacteria genomeDe novo assemblyHybrid-read assemblyLong-read-only assembly

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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbiology

Background:

  • Accurate bacterial genome assembly is crucial for understanding bacterial evolution and pathogenesis.
  • Third-Generation Sequencing (TGS) offers rapid genome assembly but struggles with circular genomes and repetitive DNA.
  • Existing assemblers are often not optimized for bacterial genomes, necessitating improved methods.

Purpose of the Study:

  • To develop an optimized method for de novo assembly of bacterial genomes.
  • To address challenges posed by circular genomes, repetitive DNA, and high error rates in long sequencing reads.
  • To create a tool capable of accurate and circularized bacterial genome assembly.

Main Methods:

  • Developed B-assembler for bacterial genome assembly using long reads or hybrid reads.
  • Employed a two-round assembly procedure involving ultra-long read selection, correction, and end-overlapping read collection.
  • Integrated optimized error correction for high-confidence assembly.

Main Results:

  • B-assembler accurately assembles circular bacterial genomes in both long-read-only and hybrid modes.
  • The method produces assemblies free of structural errors and with fewer small errors compared to other assemblers.
  • Demonstrated efficacy on both synthetic and real bacterial sequencing data.

Conclusions:

  • B-assembler offers a superior solution for bacterial genome assembly.
  • This advancement will facilitate more effective downstream bacterial genome analysis.
  • Improved bacterial genome assembly contributes to a better understanding of microbial life.