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Comparative pangenomics : analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

Comparative pangenomics : analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity


Title: Comparative pangenomics : analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity
Author: Hyun, Jason C.
Monk, Jonathan
Pálsson, Bernhard Örn
Date: 2022-01-04
Language: English
Scope:
University/Institute: University of Iceland
Series: BMC Genomics; 23(1)
ISSN: 1471-2164
DOI: https://doi.org/10.1186/s12864-021-08223-8
Subject: Líftækni; Erfðafræði; Samanburðarrannsóknir; Aminoacyl-tRNA synthetases; Comparative genomics; Core genome; Functional diversity; Heaps’ law; Multispecies; Pangenome; Protein domains; Sequence diversity; Biotechnology; Genetics
URI: https://hdl.handle.net/20.500.11815/3037

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Citation:

Hyun , J C , Monk , J & Pálsson , B Ö 2022 , ' Comparative pangenomics : analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity ' , BMC Genomics , vol. 23 , no. 1 , 7 . https://doi.org/10.1186/s12864-021-08223-8

Abstract:

Background: With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for “comparative pangenomics” that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants. Results: Applied to 12,676 genomes across 12 microbial pathogenic species, we observed several shared resolution-specific patterns of genetic diversity: First, pangenome openness is associated with species’ phylogenetic placement. Second, relationships between gene function and frequency are conserved across species, with core genomes enriched for metabolic and ribosomal genes and accessory genomes for trafficking, secretion, and defense-associated genes. Third, genes in core genomes with the highest sequence diversity are functionally diverse. Finally, certain protein domains are consistently mutation enriched across multiple species, especially among aminoacyl-tRNA synthetases where the extent of a domain’s mutation enrichment is strongly function-dependent. Conclusions: These results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.

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Publisher Copyright:© 2021, The Author(s). This research was supported by a grant from the National Institute of Allergy and Infectious Diseases (AI124316, awarded to JMM and BOP, https://www.niaid.nih.gov/). This research was also supported by a grant from the National Institutes of Health (T32GM8806, awarded to JCH, https://www.nih.gov/).

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