Bioinformatics, Comparative Genomics and Molecular Evolution
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Bioinformatics, Comparative Genomics and Molecular Evolution
A page dedicated at the dispersal of papers and facts related to these fascinating Scientific Endeavours
Curated by Arjen ten Have
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Rescooped by Arjen ten Have from Plants and Microbes
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PLOS ONE: Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition (2016)

PLOS ONE: Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wild-type Arabidopsis FLS2 confers little or no response. A targeted approach generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. These studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.


Via Kamoun Lab @ TSL
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Metagenomics: Pathogen diagnostics for the masses : Nature Reviews Genetics : Nature Publishing Group

Metagenomics: Pathogen diagnostics for the masses : Nature Reviews Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Universality of human microbial dynamics : Nature : Nature Publishing Group

Universality of human microbial dynamics : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project and the Student Microbiome Project—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.
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Rescooped by Arjen ten Have from Papers
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Beyond prebiotic chemistry

How can matter transition from the nonliving to the living state? The answer is essential for understanding the origin of life on Earth and for identifying promising targets in the search for life on other planets. Most studies have focused on the likely chemistry of RNA, protein, lipid, or metabolic “worlds” and autocatalytic sets, including attempts to make life in the lab. But these efforts may be too narrowly focused on the biochemistry of life as we know it today. A radical rethink is necessary, one that explores not just plausible chemical scenarios but also new physical processes and driving forces. Such investigations could lead to a physical understanding not only of the origin of life but also of life itself, as well as to new tools for designing artificial biology.

 

Beyond prebiotic chemistry
Leroy Cronin, Sara Imari Walker

Science  03 Jun 2016:
Vol. 352, Issue 6290, pp. 1174-1175
http://dx.doi.org/10.1126/science.aaf6310

 


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The early history and emergence of molecular functions and modular scale-free network behavior

The early history and emergence of molecular functions and modular scale-free network behavior | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold.
Arjen ten Have's insight:
Interesting view on early domain evolution. 
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Rescooped by Arjen ten Have from Plant Pathogenomics
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Scientific Reports: Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species (2016)

Scientific Reports: Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.


Via Steve Marek, Kamoun Lab @ TSL
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Encore une fois

Encore une fois | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The genomic era arrives. And this time it’s probably real
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Convergent evolution of the genomes of marine mammals : Nature Genetics : Nature Publishing Group

Convergent evolution of the genomes of marine mammals : Nature Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Andrew Foote and colleagues report the whole-genome sequences and de novo assemblies of three marine mammal species[mdash]the walrus, killer whale and manatee[mdash]and an improved bottlenose dolphin genome. Their comparative genomic analysis finds evidence of parallel evolution across the marine mammal genomes.
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This company wants to sequence your DNA and tell you your risk for 8 different cancers for $249

This company wants to sequence your DNA and tell you your risk for 8 different cancers for $249 | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The test now includes results for your hereditary risk for eight types of cancer.
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Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Publishing Group

Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
We are bacteria, YOUR resistance is futile since we will exapt. Must be a scary episode of Star Trek. This makes a lot of sense, microbes do not have sex, hence they must transfer material otherwise. These kind of studies show us how vast and how fast resistance spreads. There is even no need for direct transfer, the community will solve it. Just like the Borg they simply exapt resistance. Yet another demonstation of the fact that adatation is meaningless in terms of evolution. It is exaptation of existing plasticity.
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PLOS Computational Biology: The Maximum Entropy Fallacy Redux?

PLOS Computational Biology: The Maximum Entropy Fallacy Redux? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
Reliable modelling without threading? PLOS Computational Biology: The Maximum Entropy Fallacy Redux?
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Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation

Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
Evolutionary Trace combined with Mutual Information, now where did I see that before?
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Realizing privacy preserving genome-wide association studies

Realizing privacy preserving genome-wide association studies | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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I kind of liked Craig Venters new venture with Discovery but maybe they can learn things from this
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Evolution: Duplicate gene co-regulation slows evolution : Nature Reviews Genetics : Nature Publishing Group

Evolution: Duplicate gene co-regulation slows evolution : Nature Reviews Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Determinants of genetic diversity : Nature Reviews Genetics : Nature Publishing Group

Determinants of genetic diversity : Nature Reviews Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach

Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe . This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.
Arjen ten Have's insight:
And here comes another functional constraint at DNA level.
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Cooperation, competition and the emergence of criticality in communities of adaptive systems - IOPscience

Cooperation, competition and the emergence of criticality in communities of adaptive systems - IOPscience | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Proteogenomics connects somatic mutations to signalling in breast cancer : Nature : Nature Publishing Group

Proteogenomics connects somatic mutations to signalling in breast cancer : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Proteomics comes of age: Proteogenomics connects somatic mutations to breast cancer
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BMC Genomics: Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements (2016)

BMC Genomics: Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Background. Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one from foxtail millet (Setaria italica), three from wild foxtail millet S. viridis, and one isolate each from finger millet (Eleusine coracana), wheat (Triticum aestivum) and oat (Avena sativa), in addition to an isolate of a sister species M. grisea, that infects the wild grass Digitaria sanguinalis.

 

Results. Whole genome sequence comparison confirmed that M. oryzae Oryza and Setaria isolates form a monophyletic and close to another monophyletic group consisting of isolates from Triticum and Avena. This supports previous phylogenetic analysis based on a small number of genes and molecular markers. When comparing the host specific subgroups, 1.2–3.5 % of genes showed presence/absence polymorphisms and 0–6.5 % showed an excess of non-synonymous substitutions. Most of these genes encoded proteins whose functional domains are present in multiple copies in each genome. Therefore, the deleterious effects of these mutations could potentially be compensated by functional redundancy. Unlike the accumulation of nonsynonymous nucleotide substitutions, gene loss appeared to be independent of divergence time. Interestingly, the loss and gain of genes in pathogens from the Oryza and Setaria infecting lineages occurred more frequently when compared to those infecting Triticum and Avena even though the genetic distance between Oryza and Setaria lineages was smaller than that between Triticum and Avena lineages. In addition, genes showing gain/loss and nucleotide polymorphisms are linked to transposable elements highlighting the relationship between genome position and gene evolution in this pathogen species.

 

Conclusion. Our comparative genomics analyses of host-specific M. oryzae isolates revealed gain and loss of genes as a major evolutionary mechanism driving specialization to Oryza and Setaria. Transposable elements appear to facilitate gene evolution possibly by enhancing chromosomal rearrangements and other forms of genetic variation.


Via Kamoun Lab @ TSL
Arjen ten Have's insight:
So for all of you that keep thinking of transposable elements and alike as mere selfish genes that do not contribute to the other replicators of its host, maybe you should read this. Bummer that this happens in a pathogen.
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Detection of convergent and parallel evolution at the amino acid sequence level.

Detection of convergent and parallel evolution at the amino acid sequence level. | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Computational Modeling, Formal Analysis, and Tools for Systems Biology

Computational Modeling, Formal Analysis, and Tools for Systems Biology | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.
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Next Generation Sequencing Library Preparation: Concepts, Tips and Tricks

Next Generation Sequencing Library Preparation: Concepts, Tips and Tricks | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
In this webinar, you will learn the core steps in preparing DNA/RNA NGS libraries.
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The evolution of cooperation within the gut microbiota

Little is known about cooperative behaviour among the gut microbiota; here, limited cooperation is demonstrated for Bacteroides thetaiotaomicron, but Bacteroides ovatus is found to extracellularly digest a polysaccharide not for its own use, but to cooperatively feed other species such as Bacteroides vulgatus from which it receives return benefits.

 

The evolution of cooperation within the gut microbiota
Seth Rakoff-Nahoum, Kevin R. Foster & Laurie E. Comstock

Nature 533, 255–259 (12 May 2016) http://dx.doi.org/10.1038/nature17626


Via Complexity Digest
Arjen ten Have's insight:
This is cool stuff, and once again is shows the basics of evolution: all you need is an Evolutionary Stable Strategy and it will evolve. Unclear yes is what the benefit is (or was?).
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Functional Implications of Human-Specific Changes in Great Ape microRNAs

Functional Implications of Human-Specific Changes in Great Ape microRNAs | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing lineage-specific changes and their role in determining differences between humans and other great apes have not been specifically addressed. We analyzed the recent evolutionary history of 1,595 human microRNAs by looking at their intra- and inter-species variation in great apes using high-coverage sequenced genomes of 82 individuals including gorillas, orangutans, bonobos, chimpanzees and humans. We explored the strength of purifying selection among microRNA regions and found that the seed and mature regions are under similar and stronger constraint than the precursor region. We further constructed a comprehensive catalogue of microRNA species-specific nucleotide substitutions among great apes and, for the first time, investigated the biological relevance that human-specific changes in microRNAs may have had in great ape evolution. Expression and functional analyses of four microRNAs (miR-299-3p, miR-503-3p, miR-508-3p and miR-541-3p) revealed that lineage-specific nucleotide substitutions and changes in the length of these microRNAs alter their expression as well as the repertoires of target genes and regulatory networks. We suggest that the studied molecular changes could have modified crucial microRNA functions shaping phenotypes that, ultimately, became human-specific. Our work provides a frame to study the impact that regulatory changes may have in the recent evolution of our species.
Arjen ten Have's insight:
The authors do not claim this was the trigger for speciation but IMO this does demonstrate how sympatric speciation can occur.
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MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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