First Steps in the Analysis of Prokaryotic Pan-Genomes

Abstract

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids

“…Regardless, with an average genome size of 3 Mbp, around 3000 coding sequences, and an estimated pan-genome of 10 000 genes, we found A. baumannii to be a middle-of-the-road species among other bacteria [35]. We also note that the A.…”

“…PPanGGoLin and Panaroo also have the option to run in different modes (-defrag in PPanGGoLin, and -relaxed in Panaroo) that might allow for some adjustment without parameter tuning (Table 2); graph size decreased by 17 % (~2000 nodes) in the former (PPanGGoLin with -defrag mode) and increased by less than 5 % (~400 nodes) in the latter (Panaroo in -relaxed mode). Costa et al also report significant changes in bacterial pan-genomes when the sequence identity thresholds are altered [35]. We recommend that users try different values and settings for the parameters in these tools to improve their results.…”

Towards a better understanding of the bacterial pan-genome

“…The pan-genome is a pool of genes that may occur with different frequency among the studied group of microorganisms (Costa et al 2020;Guimarães et al 2015). Based on the frequency of their occurrence, genes are assigned to one of three groups.…”

“…The third group of genes that make up the pan-genome are unique genes, the presence of which is found only in single genomes (see Figure 1). Depending on the scope of the analysis, unique genes may be strain specific (in the pan-genome analysis of one species) or species specific (when the analysis is carried out at the inter-species level) (Costa et al 2020;Guimarães et al 2015;Mira et al 2010;Rouli et al 2015).…”

“…These genes are related to the growth environment of a bacterial species as well as the virulence of pathogenic bacteria. These genes are acquired through horizontal gene transfer, a phenomenon that can confer an adaptive advantage, and their presence can be a factor that facilitates development relative to strains lacking them (Costa et al 2020;Mira et al 2010;Rouli et al 2015).…”