Evolution by gene loss

Albalat, Ricard; Cañestro, Cristian

doi:10.1038/nrg.2016.39

Cited by 653 publications

(636 citation statements)

References 221 publications

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“…Diversification describes the generation of new genetic variation due to spontaneous mutations, gene loss and genome rearrangements, or horizontal gene transfer (HGT) (Prozorov 2001, Nemergut et al 2013, Albalat & Cañestro 2016. These processes hinge on community growth or a succession of multiple generations for genetic changes to settle in a population (Weller & Wu 2015).…”

Section: Diversificationmentioning

confidence: 99%

Microbial community assembly in marine sediments

Petro¹,

Starnawski²,

Schramm³

et al. 2017

Aquat. Microb. Ecol.

126

112

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Marine sediments are densely populated by diverse communities of archaea and bacteria, with intact cells detected kilometers below the seafloor. Analyses of microbial diversity in these unique environments have identified several dominant taxa that comprise a significant portion of the community in geographically and environmentally disparate locations. While the distributions of these populations are well documented, there is significantly less information describing the means by which such specialized communities assemble within the sediment column. Here, we review known patterns of subsurface microbial community composition and perform a meta-analysis of publicly available 16S rRNA gene datasets collected from 9 locations at depths from 1 cm to > 2 km below the surface. All data are discussed in relation to the 4 major processes of microbial community assembly: diversification, dispersal, selection, and drift. Microbial diversity in the subsurface decreases with depth on a global scale. The transition from the seafloor to the deep subsurface biosphere is marked by a filtering of populations from the surface that leaves only a subset of taxa to populate the deeper sediment zones, indicating that selection is a main mechanism of community assembly. The physiological underpinnings for the success of these persisting taxa are largely unknown, as the majority of them lack cultured representatives. Ecological explanations for the observed trends are presented, including the possible influence of energy depletion and the physiological basis of major taxonomic shifts.

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Section: Diversificationmentioning

confidence: 99%

Microbial community assembly in marine sediments

Petro¹,

Starnawski²,

Schramm³

et al. 2017

Aquat. Microb. Ecol.

126

112

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“…The continuous supply of photosynthesis-derived organic carbon by the host plant may have driven the convergent loss of the decay apparatus in ECM and AM fungi, making them more dependent on the host for carbon. Gene loss can also be an evolutionary force and a source of genetic changes that can cause adaptive phenotypic diversity (Albalat & Cañestro, 2016), and the lower complement of PCWDEs may have been an advantage in reducing plant defence responses (Plett & Martin, 2011).…”

Section: Tansley Insightmentioning

confidence: 99%

Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis?

2018

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Contents Summary1141I.Introduction1141II.The ericoid mycorrhizal lifestyle1141III.Lessons from the mycorrhizal fungal genomes1142IV.ERM fungi: a discordant voice in the mycorrhizal choir1143V.An endophytic niche for ERM fungi1144VI.Specialised vs unspecialised mycorrhizal fungi?1145VII.Conclusions and perspectives1145Acknowledgements1146References1146 Summary The genome of an organism bears the signature of its lifestyle, and organisms with similar life strategies are expected to share common genomic traits. Indeed, ectomycorrhizal and arbuscular mycorrhizal fungi share some genomic traits, such as the expansion of gene families encoding taxon‐specific small secreted proteins, which are candidate effectors in the symbiosis, and a very small repertoire of plant cell wall‐degrading enzymes. A large gene family coding for candidate effectors was also revealed in ascomycetous ericoid mycorrhizal (ERM) fungi, but these fungal genomes are characterised by a very high number of genes encoding degradative enzymes, mainly acting on plant cell wall components. We suggest that the genomic signature of ERM fungi mirrors a versatile life strategy, which allows them to occupy several ecological niches.

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“…Recently, large-scale studies based on increasing genomic data have significantly expanded the spectrum of genome reduction into a pervasive source of genetic modifications that potentially cause adaptive phenotypic diversity (10). Extensive gene loss events were observed across a wide range of organisms, including prokaryotes (11)(12)(13)(14)(15), protists (16), fungi (17,18), plants (19), and even animals (20)(21)(22)(23), thereby serving as robust evidence to support the pervasiveness of gene loss in all life kingdoms (10). However, the relative contributions of different evolutionary forces that shape the organization, structure, and diversification of microbial genomes remain elusive.…”

mentioning

confidence: 99%

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Zhang

Liu

Liang

et al. 2017

Appl Environ Microbiol

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Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillus thermosulfidooxidans. Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

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Evolution by gene loss

Cited by 653 publications

References 221 publications

Microbial community assembly in marine sediments

Microbial community assembly in marine sediments

Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis?

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

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