Why prokaryotes have pangenomes

McInerney, James O.; McNally, Alan; O’Connell, Mary J.

doi:10.1038/nmicrobiol.2017.40

Cited by 324 publications

(350 citation statements)

References 45 publications

(50 reference statements)

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“…Remarkably, most dispensable genes belonged to Mytilusspecific expanded families, and were enriched in functions related with protein/carbohydrate recognition and survival, suggesting a potential role of PAV in the evolutionary success of this cosmopolitan marine invertebrate. This unexpected discovery represents the first evidence of widespread PAV in a metazoan, extending the concept of pan-genome, so far only considered as a relevant phenomenon in viruses, prokaryotes and a few fungi and plants (15)(16)(17)(18)(19)(20)(21)(22), to the animal kingdom.…”

Section: Introductionmentioning

confidence: 77%

“…~1:3 (Figure 3C). Pan-genomes are frequently found in viruses, where they are thought to provide an evolutionary advantage by enabling a quick response to selective pressure (20), and in bacteria, where dispensable genes cover accessory functions linked with an enhanced ability of particular strains to colonize new ecological niches (18). Although the small size, simple organization and fast gene gain, loss and horizontal transfer rates of bacterial genomes (19,37) can explain the presence of a large number of dispensable genes in these organisms, pan-genomes have been also occasionally reported in plants, fungi and microalgae.…”

Section: The Mussel Pan-genomementioning

confidence: 99%

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Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Gerdol

Moreira

Cruz

et al. 2019

Preprint

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Mussels are ecologically and economically relevant edible marine bivalves, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes a core set of 45,000 genes shared by all individuals plus a surprisingly high number of dispensable genes (~15,000). The latter are subject to presence/absence variation (PAV), i.e., they may be entirely missing in a given individual and, when present, they are frequently found as a single copy. The enrichment of dispensable genes in survival functions suggests an adaptive value for PAV, which might be the key to explain the extraordinary capabilities of adaptation and invasiveness of this species. Our study underpins a unique metazoan pan-genome architecture only previously described in prokaryotes and in a few nonmetazoan eukaryotes, but that might also characterize other marine invertebrates. Significance statementIn animals, intraspecific genomic diversity is generally thought to derive from relatively small-scale variants, such as single nucleotide polymorphisms, small indels, duplications, inversions and translocations. On the other hand, large-scale structural variations which involve the loss of genomic regions encoding proteincoding genes in some individuals (i.e. presence/absence variation, PAV) have been so far only described in bacteria and, occasionally, in plants and fungi. Here we report the first evidence of a pan-genome in the animal kingdom, revealing that 25% of the genes of the Mediterranean mussel are subject to PAV. We show that this unique feature might have an adaptive value, due to the involvement of dispensable genes in functions related with defense and survival.

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Section: Introductionmentioning

confidence: 77%

Section: The Mussel Pan-genomementioning

confidence: 99%

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Gerdol

Moreira

Cruz

et al. 2019

Preprint

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“…The evolutionary impacts of HGT, by phage and other means, is an important area of microbiome research. Even when rare, HGT can have major effects 66,67 and move a single function, such as antibiotic resistance, horizontally through competing strains and species 66 .…”

Section: Microbe To Microbe: Surviving the Microbiome Junglementioning

confidence: 99%

The evolution of the host microbiome as an ecosystem on a leash

Foster

Schluter

Coyte

et al. 2017

Nature

686

616

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The human body carries vast communities of microbes that provide many benefits. Our microbiome is complex and challenging to understand, but evolutionary theory provides a universal framework with which to analyse its biology and health impacts. Here we argue that to understand a given microbiome feature, such as colonization resistance, host nutrition or immune development, we must consider how hosts and symbionts evolve. Symbionts commonly evolve to compete within the host ecosystem, while hosts evolve to keep the ecosystem on a leash. We suggest that the health benefits of the microbiome should be understood, and studied, as an interplay between microbial competition and host control.

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“…Whole-genome sequencing has revealed that in many bacteria, individual strains frequently recruit new genes from a seemingly endless genetic reservoir [1, 2]. The total complement of genes observed across all strains, known as the pan-genome, often numbers tens of thousands, up to an order of magnitude more than the number of genes present in any single genome.…”

Section: Introductionmentioning

confidence: 99%

“…The degree of gene content variation in the latter study is particularly striking as these isolates were all from the same sequence type (ST) and thus show limited nucleotide divergence in core genes and are descended from a recent common ancestor. More generally, the relationship between the size of the core and accessory genomes varies between species, with ecologically diverse species having large accessory genomes and ecologically restricted species (such as endosymbionts) having small accessory genomes [1, 2]. …”

Section: Introductionmentioning

confidence: 99%

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

et al. 2018

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BackgroundThe concept of the “pan-genome,” which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences.FindingsTo address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent (“switched”) intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli.ConclusionsFor S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).

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Why prokaryotes have pangenomes

Cited by 324 publications

References 45 publications

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

The evolution of the host microbiome as an ecosystem on a leash

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

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