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Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
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Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.

Natalie Ring1, Jonathan S Abrahams1, Miten Jain2

  • 11​Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK.

Microbial Genomics
|November 22, 2018
PubMed
Summary
This summary is machine-generated.

Long-read sequencing advances Bordetella pertussis genome assembly, revealing complex genomic rearrangements. While standard methods resolve most strains, highly complex genomes with large duplications require further optimization for complete characterization.

Keywords:
Bordetella pertussisOxford nanoporebenchmarkingduplicationsgenome assemblylong-read sequencing

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Bordetella pertussis genomes are complex, featuring high G+C content and extensive repeats.
  • Short-read sequencing struggles to resolve these complex genomic structures, leading to fragmented assemblies.
  • Long-read sequencing offers potential for complete, single-contig genome assemblies.

Purpose of the Study:

  • To evaluate long-read sequencing and analysis tools for assembling complex Bordetella pertussis genomes.
  • To identify an optimal bioinformatics pipeline for nanopore-based B. pertussis genome assembly.
  • To assess the capability of long-read sequencing in resolving genomic rearrangements and duplications.

Main Methods:

  • Utilized Oxford Nanopore R9.4 MinION flow cell with barcoding for simultaneous sequencing of five B. pertussis strains.
  • Tested various community-developed nanopore analysis tools to establish an optimal assembly pipeline.
  • Performed read mapping against the Tohama I reference genome to identify structural variations.

Main Results:

  • Achieved closed genome sequences for four out of five B. pertussis strains.
  • Visualized inter-strain genomic rearrangements, highlighting structural diversity.
  • Identified an ultra-long duplicated region (~200 kbp) in one strain and potential large duplications in another, which were not fully resolved by the standard pipeline.

Conclusions:

  • Demonstrated the utility of nanopore sequencing for resolving B. pertussis genome structure in a single run.
  • Highlighted limitations of standard library preparation for highly complex genomes with extensive duplications.
  • Recommended hybrid assembly (long and short reads) for comprehensive strain characterization and long-read-only assembly for comparative genomics.