ProPan: A Comprehensive Database for Profiling Prokaryotic Pan-genome Dynamics

NGDC  Oct 27, 2022

Compared with traditional comparative genomics analysis, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation.

Existing resources only emphasized on gene orthologs rather than representing the pan-genome dynamics of the species. Besides, some of them just included fractional prokaryotic genomic datasets and provided functions barely at the single genome level. Moreover, they overlooked that the functional annotation for a single genome can neither completely excavate the dynamics of key functional genes, nor inclusively reflect species' environmental adaptation. To address these issues, researchers from the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation) developed a prokaryotic pan-genome dynamics database, namely ProPan. This work was published online on September 28, 2022 in the journal Nucleic Acids Research, with the title "ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics".

ProPan is a public database for comprehensively profiling the characteristics in prokaryotic pan-genome dynamics. Through rigorous data quality control and large-scale data profiling, ProPan stores 23 archaeal and 1,481 bacterial species, a total of 51,882 strains genome datasets and 182,867,222 gene clusters. A variety of multi-dimensional analyses were carried out from the population perspective based on the gene clusters, including nucleotide diversity assessment of gene clusters, COG functional enrichment analysis, 31 metabolic cycle processes analyses and map construction, resistance genes prediction and PAV analyses of 126 substances (biocide, antimicrobial drug and metal), KEGG pathway association, PPI network map construction and others. Furthermore, ProPan has a very user-friendly web interface with four main modules: browse, search, statistics and downloads. To sum up, ProPan covers extensive characteristics in pan-genome dynamics of diverse prokaryotic species to offer further insights into metabolism and resistance studies.

This work was supported by the National Key Research Program of China, Strategic Priority Research Program of CAS, and National Natural Science Foundation of China.

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Dr. XIAO Jingfa
National Genomics Data Center (NGDC)