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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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Related Experiment Video

Updated: Oct 19, 2025

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus
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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

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A draft genome assembly for the eastern fox squirrel, Sciurus niger.

Lin Kang1,2, Pawel Michalak1,2,3, Eric Hallerman4

  • 1Edward Via College of Osteopathic Medicine, University of Louisiana Monroe, Monroe, LA 71203, USA.

G3 (Bethesda, Md.)
|September 22, 2021
PubMed
Summary
This summary is machine-generated.

We present the first draft genome assembly for the eastern fox squirrel (Sciurus niger), a valuable model organism. This genomic resource will advance research in behavior, ecology, adaptation, and biomedical applications.

Keywords:
Sciurus nigerde novo assemblySciuridaecandidate genescolor visioneastern fox squirrelheme biosynthesishibernationtree squirrelswhole-genome sequencing

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Area of Science:

  • Genomics
  • Mammalian Biology
  • Comparative Genomics

Background:

  • The eastern fox squirrel (Sciurus niger) displays significant geographic variation and serves as a model for behavioral and ecological studies.
  • It holds potential as a model for investigating physiological solutions to human porphyrias.

Purpose of the Study:

  • To assemble a high-quality draft genome of the eastern fox squirrel.
  • To provide a genomic resource for comparative studies, population genomics, adaptation research, and biomedical applications.

Main Methods:

  • Genome assembly utilizing Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms.
  • Gene prediction and annotation.
  • Phylogenetic analysis using maximum-likelihood methods.

Main Results:

  • A draft genome of 2.99 Gb was generated, comprising 32,830 scaffolds with an N50 of 183.8 Kb.
  • Genome completeness was estimated at 93.78%, with 24,443 protein-encoding genes predicted and 94.42% annotated.
  • Repeat elements constituted 38.49% of the genome, with LINEs, SINEs, and LTR elements being predominant.

Conclusions:

  • The eastern fox squirrel genome assembly is a valuable resource for understanding mammalian genome evolution and adaptation.
  • The genome facilitates comparative studies and holds potential for biomedical research, particularly concerning heme biosynthesis and porphyrias.
  • Analysis revealed mutations in genes related to heme biosynthesis, color vision, and hibernation, suggesting roles in ecological adaptation.