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Characterising genome architectures using Genome Decomposition Analysis

Eerik Aunin, Matthew Berriman, View ORCID ProfileAdam James Reid
doi: https://doi.org/10.1101/2021.12.01.470736
Eerik Aunin
1Wellcome Sanger Institute, Cambridge, CB10 1SA, United Kingdom
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Matthew Berriman
1Wellcome Sanger Institute, Cambridge, CB10 1SA, United Kingdom
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Adam James Reid
1Wellcome Sanger Institute, Cambridge, CB10 1SA, United Kingdom
2The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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  • ORCID record for Adam James Reid
  • For correspondence: ajr236@cam.ac.uk
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Abstract

Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes.

Significance Genome sequencing has revealed that there are functionally important arrangements of genes, repetitive elements and regulatory sequences within chromosomes. Identifying these arrangements requires extensive computation and analysis. Furthermore, improvements in genome sequencing technology and the establishment of consortia aiming to sequence all species of eukaryotes mean that there is a need for high throughput methods for discovering new genome biology. Here we present a software pipeline, named GDA, which determines the patterns of genomic features across chromosomes and uses these to characterise genome architecture. We show that it recapitulates the known genome architecture of several Apicomplexan parasites and use it to identify features in a recently sequenced, less well-characterised genome. GDA scales well to large genomes and is freely available.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/eeaunin/gda

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 02, 2021.
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Characterising genome architectures using Genome Decomposition Analysis
Eerik Aunin, Matthew Berriman, Adam James Reid
bioRxiv 2021.12.01.470736; doi: https://doi.org/10.1101/2021.12.01.470736
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Characterising genome architectures using Genome Decomposition Analysis
Eerik Aunin, Matthew Berriman, Adam James Reid
bioRxiv 2021.12.01.470736; doi: https://doi.org/10.1101/2021.12.01.470736

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