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Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

Cited 6 time in Web of Science Cited 7 time in Scopus
Authors
Park, Sang-Cheol; Lee, Kihyun; Kim, Yeong Ouk; Won, Sungho; Chun, Jongsik
Issue Date
2019-04
Citation
Frontiers in Microbiology, Vol.10, p. 834
Keywords
pan-genomecore-genomeHeaps' lawgene poollarge-scale genomicsseven speciesestimation model
Abstract
For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified, because most studies have used a small number of genomes. Here, we constructed pan-genomes of seven species in order to elucidate variations in the genetic contents of >27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella spp., Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, and Acinetobacter baumannii. This work showed the pan-genomes of all seven species has open property. Additionally, systematic evaluation of the characteristics of their pan-genome revealed that phylogenetic distance provided valuable information for estimating the parameters for pan-genome size among several models including Heaps' law. Our results provide a better understanding of the species and a solution to minimize sampling biases associated with genome-sequencing preferences for pathogenic strains.
ISSN
1664-302X
URI
https://hdl.handle.net/10371/165724
DOI
https://doi.org/10.3389/fmicb.2019.00834
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College of Natural Sciences (자연과학대학)Dept. of Biological Sciences (생명과학부)Journal Papers (저널논문_생명과학부)
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