Bioinformatics, Comparative Genomics and Molecular Evolution
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Rescooped by Arjen ten Have from Plant Pathogenomics
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Frontiers: Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors (2014)

Frontiers: Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors (2014) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control.


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Bioinformatics, Comparative Genomics and Molecular Evolution
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Clinical Knowledgebase (CKB)

Clinical Knowledgebase (CKB) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

JAX-CKB is a powerful tool for interpreting complex genomic profiles, and represents a valuable resource for clinicians and translational and clinical researchers. JAX-CKB advances JAX’s mission to discover genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.


jaxmoleculardx@jax.org | 1.860.837.2320
Arjen ten Have's insight:
Future of personalized medicine includes comparative analysis for which we need to gather data and make them available for medical teams (i.e. that lack knowledge in Bioinformatics). We will also need bioinformaticians specialized in medicine.
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Alternative evolutionary histories in the sequence space of an ancient protein

Alternative evolutionary histories in the sequence space of an ancient protein | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Arjen ten Have's insight:
Joe Thornton strikes again. He is the leader in ancestral sequence  reconstruction and now exploited the brilliant idea of letting an ancestral sequence evolve. "To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not." " We find hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history."

Amazing and in full concordance with the work of that other brilliant evolutionary biologist, Andreas Wagner. Iḿ Flabbergasted!
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The dark side of the human genome : Nature : Nature Research

The dark side of the human genome : Nature : Nature Research | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Scientists are uncovering the hidden switches in our genome that dial gene expression up and down, but much work lies ahead to peel back the many layers of regulation.
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RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Kelsic et al. develop and apply MAGE-seq to identify RNA structures that determine optimal codon preferences in an essential E. coli gene.
Arjen ten Have's insight:
Yet another type of functional constraint acting at the level of translation efficiency. or is it rna stability?
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Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor
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Genome Expression Balance in a Triploid Trihybrid Vertebrate | Genome Biology and Evolution | Oxford Academic

Arjen ten Have's insight:
Sex is the emerging property of evolution. It is not meant for propagation but rather for maintaining high variation.
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Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014)

Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.


Via Kamoun Lab @ TSL
Arjen ten Have's insight:
Sharing stuff is key yo any interaction. The higher the mutual dependency, the more partners will share. What I do not have clear yet is whether pathogenic relationships will differ substantially from mutualistic ones. miRNA has been shown in plant pathogen relationships, but I can also envisage these in a mutualistic symbiosis. Quite a conundrum. But that' s what  plant-pathogen relations are about anyway.
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The genotype-phenotype map of an evolving digital organism

The genotype-phenotype map of an evolving digital organism | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Author summary The phenotype of an organism comprises the set of morphological and functional traits encoded by its genome. In natural evolving systems, phenotypes are organized into mutationally connected networks of genotypes, which increase the likelihood for an evolving population to encounter novel adaptive phenotypes (i.e., its evolvability). We do not know whether artificial systems, such as self-replicating and evolving computer programs—digital organisms—are more or less evolvable than natural systems. By studying how genotypes map onto phenotypes in digital organisms, we characterize many commonalities between natural and artificial evolving systems. In addition, we show that phenotypic complexity can both facilitate and constrain evolution, which harbors lessons not only for designing evolvable artificial systems, but also for synthetic biology.
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Proteins: Structure, Function, and Bioinformatics - Volume 85, Issue 3 - Sixth Meeting on the Critical Assessment of Predicted Interactions - Wiley Online Library

Proteins: Structure, Function, and Bioinformatics - Volume 85, Issue 3 - Sixth Meeting on the Critical Assessment of Predicted Interactions - Wiley Online Library | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events

National Academy of Sciences
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The Evolutionary Origins of Hierarchy

The Evolutionary Origins of Hierarchy | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Author Summary Hierarchy is a ubiquitous organizing principle in biology, and a key reason evolution produces complex, evolvable organisms, yet its origins are poorly understood. Here we demonstrate for the first time that hierarchy evolves as a result of the costs of network connections. We confirm a previous finding that connection costs drive the evolution of modularity, and show that they also cause the evolution of hierarchy. We further confirm that hierarchy promotes evolvability in addition to evolvability caused by modularity. Because many biological and human-made phenomena can be represented as networks, and because hierarchy is a critical network property, this finding is immediately relevant to a wide array of fields, from biology, sociology, and medical research to harnessing evolution for engineering.
Arjen ten Have's insight:
Hierarchy evolves as a result of connection cost. How cool!
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An efficient system to fund science: from proposal review to peer-to-peer distributions

An efficient system to fund science: from proposal review to peer-to-peer distributions | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

This paper presents a novel model of science funding that exploits the wisdom of the scientific crowd. Each researcher receives an equal, unconditional part of all available science funding on a yearly basis, but is required to individually donate to other scientists a given fraction of all they receive. Science funding thus moves from one scientist to the next in such a way that scientists who receive many donations must also redistribute the most. As the funding circulates through the scientific community it is mathematically expected to converge on a funding distribution favored by the entire scientific community. This is achieved without any proposal submissions or reviews. The model furthermore funds scientists instead of projects, reducing much of the overhead and bias of the present grant peer review system. Model validation using large-scale citation data and funding records over the past 20 years show that the proposed model could yield funding distributions that are similar to those of the NSF and NIH, and the model could potentially be more fair and more equitable. We discuss possible extensions of this approach as well as science policy implications.

 

An efficient system to fund science: from proposal review to peer-to-peer distributions

Johan Bollen, David Crandall, Damion Junk, Ying Ding, Katy Börner

Scientometrics (2016). doi:10.1007/s11192-016-2110-3


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Control principles of complex systems

Control principles of complex systems | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

A reflection of our ultimate understanding of a complex system is our ability to control its behavior. Typically, control has multiple prerequisites: it requires an accurate map of the network that governs the interactions between the system’s components, a quantitative description of the dynamical laws that govern the temporal behavior of each component, and an ability to influence the state and temporal behavior of a selected subset of the components. With deep roots in dynamical systems and control theory, notions of control and controllability have taken a new life recently in the study of complex networks, inspiring several fundamental questions: What are the control principles of complex systems? How do networks organize themselves to balance control with functionality? To address these questions here recent advances on the controllability and the control of complex networks are reviewed, exploring the intricate interplay between the network topology and dynamical laws. The pertinent mathematical results are matched with empirical findings and applications. Uncovering the control principles of complex systems can help us explore and ultimately understand the fundamental laws that govern their behavior.

 

Control principles of complex systems
Yang-Yu Liu and Albert-László Barabási
Rev. Mod. Phys. 88, 035006


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Molecular Evolution of Antifungal Drug Resistance | Annual Review of Microbiology

Molecular Evolution of Antifungal Drug Resistance | Annual Review of Microbiology | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Wham: Identifying Structural Variants of Biological Consequence

Wham: Identifying Structural Variants of Biological Consequence | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
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Epigenetics and the evolution of instincts

Epigenetics and the evolution of instincts | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
An animal mind is not born as an empty canvas: Bottlenose dolphins know how to swim and honey bees know how to dance without ever having learned these skills. Little is known about how animals acquire the instincts that enable such innate behavior. Instincts are widely held to be ancestral to learned behavior. Some have been elegantly analyzed at the cellular and molecular levels, but general principles do not exist. Based on recent research, we argue instead that instincts evolve from learning and are therefore served by the same general principles that explain learning.
Arjen ten Have's insight:
Not a big fan of epigenetics, this makes sense. Moreover, it would be a more feasible explanation for the language instinct than Chomsky' s hypothesis (indeed not a theory) thst claims we are hardwired. Epigenetics would be a go between.
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Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.
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Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor
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Membrane fission by protein crowding

National Academy of Sciences
Arjen ten Have's insight:
This makes a lot of sense and can explain how effectors are trafficked. Proteins are selected based on a certain subsequence, gathered and send to (where ever they need to go). BI can help identifying these subsequences.
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Post-molecular systematics and the future of phylogenetics

Post-molecular systematics and the future of phylogenetics https://t.co/yZfMZsI97b (RT not an endorsement, remember...)
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Very interesting, for once a review that tackles the dataside of phylogeny.
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Niche construction in evolutionary theory: the construction of an academic niche?

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Arjen ten Have's insight:
where preprints go wrong. The construction of an academic niche? This is meant as an insult and i wonder based on what. Niche construction is like Wrights hypothesis of balanced shift very much to be seen as a metaphor.
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Rathenau Platz's comment, March 29, 2:44 AM
1. Niche construction has not been used as a metaphor, at least not by its major proponents. It has been represented as a process at par with Natural Selection.
Rathenau Platz's comment, March 29, 2:46 AM
2. Wright's shifting Balance Theory is not a metaphor either (fitness landscapes probably are).
Arjen ten Have's comment, March 29, 9:23 AM
It seems you miss my point. Let me start by stating I am not a fan of niche construction. Then 2 Wright's shifting balance theory is a theory, hence accepted by consensus. Nevertheless, it is impossible to prove it since we do not have valid knowledge on Ne or s. Hence, it's generally value is found by understanding it as a metaphor. Theb 1. The fact that it's major proponents do not use it as a metaphor does not mean it should not be seen as a metaphor. I can even understand Sheldrake's morfofield hypothesis as a metaphor, ridiculous as it is. The point I am trying to make is that certain theories are not so easy to prove or reject. No matter how stupid you might find an hypothesis, claiming it is part of constructing an academic niche is not nice AND does not add. Not even Deepak Choprah is doing that, he actually believes what he claims. Serious reviewers would insist on taking this out of the MS, and that is where preprints go wrong in this era of information explosion.
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eLife: Codon optimization underpins generalist parasitism in fungi (2017)

eLife: Codon optimization underpins generalist parasitism in fungi (2017) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasite. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long term persistence of generalist parasitism.


Via Kamoun Lab @ TSL
Arjen ten Have's insight:
Does this suggest specialists do not have the time to evolve codon optimization? Evolution does not cease to surprise me!
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Genome Biology and Evolution: A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi (2016)

Genome Biology and Evolution: A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Smut fungi are plant pathogens mostly parasitizing wild species of grasses as well as domesticated cereal crops. Genome analysis of several smut fungi including Ustilago maydis revealed a singular clustered organization of genes encoding secreted effectors. In U. maydis, many of these clusters have a role in virulence. Reconstructing the evolutionary history of clusters of effector genes is difficult because of their intrinsically fast evolution, which erodes the phylogenetic signal and homology relationships. Here, we describe the use of comparative evolutionary analyses of quality draft assemblies of genomes to study the mechanisms of this evolution. We report the genome sequence of a South African isolate of Sporisorium scitamineum, a smut fungus parasitizing sugar cane with a phylogenetic position intermediate to the two previously sequenced species U. maydisand Sporisorium reilianum. We show that the genome of S. scitamineumcontains more and larger gene clusters encoding secreted effectors than any previously described species in this group. We trace back the origin of the clusters and find that their evolution is mainly driven by tandem gene duplication. In addition, transposable elements play a major role in the evolution of the clustered genes. Transposable elements are significantly associated with clusters of genes encoding fast evolving secreted effectors. This suggests that such clusters represent a case of genome compartmentalization that restrains the activity of transposable elements on genes under diversifying selection for which this activity is potentially beneficial, while protecting the rest of the genome from its deleterious effect.


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Bridget Barker's curator insight, February 2, 11:17 AM
Using this for my microbial ecology course
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The Strange Inevitability of Evolution

The Strange Inevitability of Evolution | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Ah, but isn’t all this wonder simply the product of the blind fumbling of Darwinian evolution, that mindless machine which takes random variation and sieves it by natural selection? Well, not quite. You don’t have to be a benighted creationist, nor even a believer in divine providence, to argue that Darwin’s astonishing theory doesn’t fully explain why nature is so marvelously, endlessly inventive. “Darwin’s theory surely is the most important intellectual achievement of his time, perhaps of all time,” says evolutionary biologist Andreas Wagner of the University of Zurich. “But the biggest mystery about evolution eluded his theory. And he couldn’t even get close to solving it.”

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Mustread for every biologist
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Can we open the black box of AI?

Can we open the black box of AI? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Artificial intelligence is everywhere. But before scientists trust it, they first need to understand how machines learn.

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