Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Maistrenko, Oleksandr M.; Mende, Daniel R.; Lϋetge, Mechthild; Hildebrand, Falk; Schmidt, Thomas Sebastian Benedikt; Li, Simone S.; Coelho, Luís Pedro; Huerta-Cepas, Jaime; Sunagawa, Shinichi; Bork, Peer

doi:10.1101/735696

Cited by 4 publications

(3 citation statements)

References 70 publications

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“…Such transfers are thought to facilitate adaptation to the environment. Consistent with this hypothesis, environment and lifestyle are found to correlate with intra-species genomic variation in prokaryotes 43 . Interestingly, several studies have found that some ribosomal proteins are often transferred 23,33 , which runs against received wisdom and the complexity hypothesis, but is consistent with prior research suggesting that informational genes can in fact undergo lateral gene transfer 44 and appears to confi rm the suspicions of tree of life critics 4 .…”

Section: Lateral Gene Transfer Is Endemic Across the Tree Of Lifesupporting

confidence: 56%

The past, present and future of the tree of life

Blais

Archibald

2021

Current Biology

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Section: Lateral Gene Transfer Is Endemic Across the Tree Of Lifesupporting

confidence: 56%

The past, present and future of the tree of life

Blais

Archibald

2021

Current Biology

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“…Recently, prokaryotic pan-genomes have crossed species and even phyla boundaries, including one study using 7,104 genomes from ten prokaryotic phyla 79 . Due to the small size of haploid prokaryotic genomes such studies are computationally feasible.…”

Section: Prospects and Future Directionsmentioning

confidence: 99%

Plant pan-genomes are the new reference

et al. 2020

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Recent years have seen a surge in plant genome sequencing projects and the comparison of multiple related individuals. The high degree of genomic variation observed led to the realisation that single reference genomes do not represent the diversity within a species, and led to the expansion of the pan-genome concept. Pan-genomes represent the genomic diversity of a species and includes core genes, found in all individuals, as well as variable genes which are absent in some individuals. Variable gene annotations often show similarities across plant species, with genes for biotic and abiotic stress commonly enriched within variable gene groups. Here we review the growth of pan-genomics in plants, explore the origins of gene presence/absence variation and show how pan-genomes can support plant breeding and evolution studies. Pan-genomes in plants: beginnings and current statusThe concept of pan-genomes was first developed in bacteria in 2005 1 , where the sequencing of several isolates of Streptococcus agalactiae revealed a core genome represented by 80% of S. agalactiae genes, with the other 20% being absent in at least one isolate 1 . However, it took almost 10 years for plant pan-genomes to be constructed after the initial bacterial pangenome work. This was partially due to the expense of data generation, but also the expectation that there would be very little gene presence/absence variation (PAV) in higher organisms which do not exchange genetic material as freely as bacteria 2 . The first publication to apply the term pan-genome in plants appeared in 2007, where it described short variable regions in the rice and maize genomes 3 . However, the extent of gene presence/absence was not understood at that time due to lack of accurate whole genome assemblies for multiple individuals of the same species. However, as DNA sequencing costs declined, it became feasible to undertake whole genome comparisons within species, and three general approaches for pan-genome assembly were developed 4,5 (Figure 1). The first method developed was the whole genome assembly and comparison, where the genomes of multiple individuals are assembled and then compared. This was later complemented by the iterative assembly and presence/absence variation calling approach, where genomic reads from multiple individuals are aligned to a reference, and non-aligning reads assembled and added to the growing pan-genome reference. Subsequent remapping of all reads to the pan-genome permits PAV calling across the population. More recently there have been rapid developments in graph based pan-genome assembly, where a graph representing genomic diversity and conservation is constructed 6 .

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“…S7B). While pangenome sizes are known to vary between species (15,17,34), it is intriguing to find such extensive gene content variation within a single population and local source. These results also corroborate observations from a previous study of another large Sal.…”

Section: Discussionmentioning

confidence: 99%

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

Conrad

Viver

Gago

et al. 2021

Preprint

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Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological mechanisms that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to environmental perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes recovered from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of these ecosystems. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (non-core) genes showed low in situ coverage based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or ephemeral, 3.49% of them became abundant when salinity (but not light intensity) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results revealed a possible mechanism for how this immense gene diversity is maintained, which has implications for the prokaryotic species concept.

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Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Cited by 4 publications

References 70 publications

The past, present and future of the tree of life

The past, present and future of the tree of life

Plant pan-genomes are the new reference

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

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