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Reference-based QUantification Of gene Dispensability (QUOD)

View ORCID ProfileKatharina Sielemann, View ORCID ProfileBernd Weisshaar, View ORCID ProfileBoas Pucker
doi: https://doi.org/10.1101/2020.04.28.065714
Katharina Sielemann
1Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
2Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615 Bielefeld, Germany
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Bernd Weisshaar
1Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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  • For correspondence: bernd.weisshaar@uni-bielefeld.de
Boas Pucker
1Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
3Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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Abstract

Background Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to ‘conditionally dispensable’, this concept still requires the assignment of genes to distinct groups.

Results Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores.

Conclusions Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email addresses: kfrey{at}cebitec.uni-bielefeld.de, bpucker{at}cebitec.uni-bielefeld.de, bernd.weisshaar{at}uni-bielefeld.de

  • This is the revised version of our manuscript.

  • https://github.com/ksielemann/QUOD

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 4.0 International license.
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Posted November 27, 2020.
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Reference-based QUantification Of gene Dispensability (QUOD)
Katharina Sielemann, Bernd Weisshaar, Boas Pucker
bioRxiv 2020.04.28.065714; doi: https://doi.org/10.1101/2020.04.28.065714
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Reference-based QUantification Of gene Dispensability (QUOD)
Katharina Sielemann, Bernd Weisshaar, Boas Pucker
bioRxiv 2020.04.28.065714; doi: https://doi.org/10.1101/2020.04.28.065714

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