Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera

Abstract

BackgroundThe increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria.ResultsA variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets". We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer. Finally, core proteomes and unique proteomes were used to study the proteomic cohesiveness of several bacterial species, revealing that some bacterial species had little cohesiveness in their protein content, with some having fewer proteins unique to that species than randomly-chosen sets of isolates from the same genus.ConclusionsThe results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.

Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

“…Our data suggest that a pangenome based approach applied to whole genome sequences can not only identify conserved genome regions but also detect rich information on genomic differences existing within strains of same species as has also been shown from previous comparative genomic studies on Mtb [ 35 , 48 , 51 ]. In a recent study by Liu et al , a comparative analysis of 7 newly sequenced clinical isolates and 7 complete reference genomes of Mtb showed that genomic variations might play an important role in the genomic plasticity of Mtb [ 35 ].…”

“…The variable component of the pangenome comprised of 4,725 gene clusters. Previous studies performed by Trost et al and Zakham et al on fourteen and twenty one mycobacterial genomes respectively have also shown that the mycobacteria has a fairly small core genome as compared to the accessory genome component [ 48 , 51 ]. From the accessory genome, a subset of 74 clusters was identified which was not represented in the reference laboratory templates, Mtb ATCC H37Rv and Mtb ATCC H37Ra, but were present in most of the clinical isolates being analyzed.…”

Telling the whole story in a 10,000-genome world

“…Figure 3a shows the increase in the number of homologous sets of proteins as additional members of specific genera are sampled, for 20 genera with at least ten sequenced representatives each. Within this group, Brucella is a notable outlier (also noted by [ 36 ]) with the tenth added genome increasing the count of homologous sets by < 1%. This suggests that the sampled members of Brucella are largely clonal, with little variation in gene content.…”

“…This meaning is closest to the pan-genome idea of your citation [ 35 ]. But "novel genes" should be distinguished from novel gene families and from novel proteins ([ 36 ] explicitly uses proteins instead of genes in their measure of novelty but then discusses the "proteome"). A novel protein can come from a previously known gene and a novel gene can come from a previously known gene family.…”

Whole Genome Annotation: In Silico Analysis

“…The problems a researcher would normally encounter when utilizing annotations from various genomes could be resolved by comparison with the annotation of a homologous organism. This situation is common when one examines the pangenome of a species, as it is expected that most of the coding sequences of different strains of bacteria are not very different (Trost et al, 2010). In this case, it appears to be advantageous to identify a small set of target organisms (subject) in a sequence similarity search, with the objective of providing a first genome annotation (query); this may even be a set with only one organism.…”