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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Targeted DNA Methylation Analysis by Next-generation Sequencing
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Genome-wide methylation patterns from canine nanopore assemblies.

Peter Z Schall1,2, Paige A Winkler3, Simon M Petersen-Jones3

  • 1Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.

G3 (Bethesda, Md.)
|September 8, 2023
PubMed
Summary

New canine genome assemblies using Oxford Nanopore sequencing improve continuity and reveal missing conserved genes. This advancement aids in understanding canine genetic disorders and epigenetic profiles.

Keywords:
Oxford Nanoporede novo assemblylongread sequencingmethylation

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Area of Science:

  • Genomics
  • Comparative Genomics
  • Epigenetics

Background:

  • Long-read sequencing advances enable high-quality genome assemblies.
  • Eight long-read canine genome assemblies exist, but comparisons are limited.
  • Specific dog breeds have enriched, unresolved genetic disorders.

Purpose of the Study:

  • To generate high-quality de novo canine genome assemblies using Oxford Nanopore sequencing.
  • To compare newly generated assemblies with existing canine genome assemblies.
  • To analyze genome-wide methylation profiles and identify conserved genes.

Main Methods:

  • Oxford Nanopore long-read sequencing for de novo assembly.
  • Utilized published data to generate a new Labrador Retriever assembly.
  • Uniform assessment of 8 existing assemblies for quality, divergence, and BUSCO.
  • Generated genome-wide methylation profiles from nanopore sequencing.

Main Results:

  • Generated 3 new high-quality de novo assemblies (2 Bernese Mountain Dogs, 1 Cairn terrier).
  • Achieved a ~280-fold increase in continuity for a Labrador Retriever assembly.
  • Identified ~400 conserved genes missing across all assessed assemblies.
  • Nanopore sequencing provided broad concordance with bisulfite sequencing for methylation, with superior mobile element coverage.

Conclusions:

  • Oxford Nanopore sequencing is effective for resolving canine genome sequence and epigenetic profiles.
  • New assemblies enhance the understanding of canine genetics, particularly for breeds with genetic disorders.
  • The identification of missing conserved genes highlights areas for future genomic research in dogs.