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An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth.

Cassandria G Tay Fernandez1, Jacob I Marsh1, Benjamin J Nestor1

  • 1Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.

Methods in Molecular Biology (Clifton, N.J.)
|July 11, 2022
PubMed
Summary

Presence-absence variants (PAVs) are key genomic differences found in some individuals but not others. This study presents a method using sequence alignment and Mosdepth to identify PAVs, aiding in genomic diversity and evolutionary studies.

Keywords:
Gene lossPresence–absence variantsSGSGeneLossSingle-nucleotide polymorphisms

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Presence-absence variants (PAVs) represent significant structural variations within a species' genome.
  • PAVs contribute to genomic diversity and are associated with specific traits and evolutionary history, particularly in bacteria and plants.

Purpose of the Study:

  • To detail a method for identifying PAVs by aligning short-read sequence data to a reference genome or pangenome.
  • To introduce the use of the Mosdepth tool for calculating sequencing coverage to detect PAVs.

Main Methods:

  • Sequence reads are aligned to a reference genome or pangenome assembly.
  • Sequencing coverage is analyzed using Mosdepth to identify regions with absent reads, indicating PAVs.
  • A PAV table is constructed for subsequent comparative genomic analyses.

Main Results:

  • The described method effectively identifies PAVs through read alignment and coverage analysis.
  • Mosdepth facilitates the accurate calculation of sequencing coverage for PAV detection.
  • A comprehensive PAV table can be generated for downstream research.

Conclusions:

  • The presented methodology provides a robust approach for PAV identification and analysis.
  • This method enhances the study of genomic diversity and evolutionary trajectories.
  • PAV analysis is crucial for understanding trait variation and species evolution.