AUTHOR=Park Sang-Cheol , Lee Kihyun , Kim Yeong Ouk , Won Sungho , Chun Jongsik 

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

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.00834

DOI=10.3389/fmicb.2019.00834

ISSN=1664-302X

ABSTRACT=<p>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 &gt;27,000 genomes belonging to <italic>Streptococcus pneumoniae</italic>, <italic>Staphylococcus aureus</italic> subsp. <italic>aureus</italic>, <italic>Salmonella enterica</italic> subsp. <italic>enterica</italic>, <italic>Escherichia coli</italic> and <italic>Shigella</italic> spp., <italic>Mycobacterium tuberculosis</italic> complex, <italic>Pseudomonas aeruginosa</italic>, and <italic>Acinetobacter baumannii.</italic> 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.</p>